data_4213
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Retro-inverso analogue of G-H loop of VP1 in FMD virus
;
_BMRB_accession_number 4213
_BMRB_flat_file_name bmr4213.str
_Entry_type original
_Submission_date 1998-05-23
_Accession_date 1998-05-23
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details .
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Petit M. C. .
2 Benkirane N. . .
3 Guichard G. . .
4 'Phan Chan Du' A. . .
5 Cung M. T. .
6 Briand J. P. .
7 Muller S. . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 102
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2008-07-11 update BMRB 'Updating non-standard residue'
2008-03-24 update BMRB .
2000-03-10 original author .
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Solution structure of a retro-inverso peptide analogue mimicking the
foot-and-mouth disease virus major antigenic site. Structural basis for its
antigenic cross-reactivity with the parent peptide.
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code 99121111
_PubMed_ID ?
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Petit M. C. .
2 Benkirane N. . .
3 Guichard G. . .
4 'Phan Chan Du' A. . .
5 Cung M. T. .
6 Briand J. P. .
7 Muller S. . .
stop_
_Journal_abbreviation 'J. Biol. Chem.'
_Journal_name_full 'Journal of Biological Chemistry'
_Journal_volume 274
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 3686
_Page_last 3692
_Year 1999
_Details .
loop_
_Keyword
antigen
FMDV
peptidomimetic
retro-inverso
stop_
save_
##################################
# Molecular system description #
##################################
save_A_system
_Saveframe_category molecular_system
_Mol_system_name 'retro-inverso peptide'
_Abbreviation_common peptide
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'retro-inverso peptide' $A
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state monomer
_System_paramagnetic no
_System_thiol_state 'not present'
_Database_query_date .
_Details
;
This peptide is a synthetic peptide. It sequence corresponds to the major
immunogen region of the Foot-and-Mouth-Disease Virus (FMDV) serotype A variant
USA. The goal of this study is to develop a peptide that can be used as a
synthetic vaccine. For this reason the authors used a retro-inverso strategy in
order to enhance its stability in vivo.
Retro-inverso means that it was synthesized using D-residues and sequence was
inverted regarding the sequence in the protein (parent peptide - see 1bcv ).
The idea is to keep the orientations of the residues side-chains as it is in
the parent peptide. For more details about the retro-inverso peptides, the
antigenicity and immunogenicity of retro-inverso petidomimetics please see
Guichard et al. (1994) Proc. Natl.Acad. Sci. USA , 91, pp 9765-9769 Muller et
al. (1995) Peptide Research, 8 pp 138-144.
The parent peptide corresponds to the sequence 141-159 of VP1 protein of the
capsid of FMD virus. In this retro-inverso peptide the numbering of the
residues is made as following : 159 is at its N-terminal part , it correspond
to a isobutyl-malonate (LML) in order to mimic the C-terminal part of the
parent peptide; At the C-terminal part of the retro-inverso peptidomimetics
NH2-CO (CAG) was added in order to mimic the N-terminal of the parent peptide.
The Het group NH2-CO has the number 140.
All non glycine residues present a D configuration. MLEU presents a L
configuration, because it occurred less restraints violations during DYANA
calculations than the D isomer.
'LML was introduced in DYANA library as well as D-residues.' 'PHI angles of
D-residues were set in the [10,170] interval during structure calculations.'
In this peptide we found that the only the region from 151 to 159 is exhibiting
structural motifs which are untypical beta-turns. 6 betas turns were found
involving the following residues : 156-159 for 53 % of the structures, 155-158
for 30% of the structures , 153-156 for 46 % of the structures, 151-154 for 53%
of the structures, 148-151 for 30% of the structures and 145-148 (RGD) for 13 %
of the structures. The optimal fit on backbone atoms was found on the 150-158
region with a rmsd of 0.8 A.
;
save_
########################
# Monomeric polymers #
########################
save_A
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common 'retro-inverso peptide'
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details 'CONH2 is covalently attached to the C terminal glycine G141 by an amide linkage.'
##############################
# Polymer residue sequence #
##############################
_Residue_count 20
_Mol_residue_sequence
;
XXXXXXXXXXGXXGXXGXGX
;
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 159 LML 2 158 DGN 3 157 DAR 4 156 DAL 5 155 DVA
6 154 DAR 7 153 DPR 8 152 DAL 9 151 DLE 10 150 DSN
11 149 GLY 12 148 DPN 13 147 DAS 14 146 GLY 15 145 DAR
16 144 DVA 17 143 GLY 18 142 DSN 19 141 GLY 20 140 NH2
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
######################
# Polymer residues #
######################
save_chem_comp_DSN
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-SERINE
_BMRB_code .
_PDB_code DSN
_Standard_residue_derivative .
_Molecular_mass 105.093
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 11:48:02 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
CB CB C . 0 . ?
OG OG O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HXT HXT H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HG HG H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA C ? ?
SING CA CB ? ?
SING CA HA ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
SING CB OG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
SING OG HG ? ?
stop_
save_
save_chem_comp_DGN
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-GLUTAMINE
_BMRB_code .
_PDB_code DGN
_Standard_residue_derivative .
_Molecular_mass 146.144
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 11:49:35 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD CD C . 0 . ?
OE1 OE1 O . 0 . ?
NE2 NE2 N . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HXT HXT H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HG2 HG2 H . 0 . ?
HG3 HG3 H . 0 . ?
HE21 HE21 H . 0 . ?
HE22 HE22 H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA C ? ?
SING CA CB ? ?
SING CA HA ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
SING CG CD ? ?
SING CG HG2 ? ?
SING CG HG3 ? ?
DOUB CD OE1 ? ?
SING CD NE2 ? ?
SING NE2 HE21 ? ?
SING NE2 HE22 ? ?
stop_
save_
save_chem_comp_DVA
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-VALINE
_BMRB_code .
_PDB_code DVA
_Standard_residue_derivative .
_Molecular_mass 117.146
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 11:52:13 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
CG1 CG1 C . 0 . ?
CG2 CG2 C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HB HB H . 0 . ?
HG11 HG11 H . 0 . ?
HG12 HG12 H . 0 . ?
HG13 HG13 H . 0 . ?
HG21 HG21 H . 0 . ?
HG22 HG22 H . 0 . ?
HG23 HG23 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB CG1 ? ?
SING CB CG2 ? ?
SING CB HB ? ?
SING CG1 HG11 ? ?
SING CG1 HG12 ? ?
SING CG1 HG13 ? ?
SING CG2 HG21 ? ?
SING CG2 HG22 ? ?
SING CG2 HG23 ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_DAR
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-ARGININE
_BMRB_code .
_PDB_code DAR
_Standard_residue_derivative .
_Molecular_mass 175.209
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 11:53:57 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD CD C . 0 . ?
NE NE N . 0 . ?
CZ CZ C . 0 . ?
NH1 NH1 N . 0 . ?
NH2 NH2 N . 1 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HG2 HG2 H . 0 . ?
HG3 HG3 H . 0 . ?
HD2 HD2 H . 0 . ?
HD3 HD3 H . 0 . ?
HE HE H . 0 . ?
HH11 HH11 H . 0 . ?
HH12 HH12 H . 0 . ?
HH21 HH21 H . 0 . ?
HH22 HH22 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
SING CG CD ? ?
SING CG HG2 ? ?
SING CG HG3 ? ?
SING CD NE ? ?
SING CD HD2 ? ?
SING CD HD3 ? ?
SING NE CZ ? ?
SING NE HE ? ?
SING CZ NH1 ? ?
DOUB CZ NH2 ? ?
SING NH1 HH11 ? ?
SING NH1 HH12 ? ?
SING NH2 HH21 ? ?
SING NH2 HH22 ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_DAS
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common 'D-ASPARTIC ACID'
_BMRB_code .
_PDB_code DAS
_Standard_residue_derivative .
_Molecular_mass 133.103
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 11:59:20 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
OD1 OD1 O . 0 . ?
OD2 OD2 O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HD2 HD2 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA C ? ?
SING CA CB ? ?
SING CA HA ? ?
DOUB C O ? ?
SING C OXT ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
DOUB CG OD1 ? ?
SING CG OD2 ? ?
SING OD2 HD2 ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_DPN
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-PHENYLALANINE
_BMRB_code .
_PDB_code DPN
_Standard_residue_derivative .
_Molecular_mass 165.189
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 12:00:47 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD1 CD1 C . 0 . ?
CD2 CD2 C . 0 . ?
CE1 CE1 C . 0 . ?
CE2 CE2 C . 0 . ?
CZ CZ C . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HXT HXT H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HD1 HD1 H . 0 . ?
HD2 HD2 H . 0 . ?
HE1 HE1 H . 0 . ?
HE2 HE2 H . 0 . ?
HZ HZ H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA C ? ?
SING CA CB ? ?
SING CA HA ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
DOUB CG CD1 ? ?
SING CG CD2 ? ?
SING CD1 CE1 ? ?
SING CD1 HD1 ? ?
DOUB CD2 CE2 ? ?
SING CD2 HD2 ? ?
DOUB CE1 CZ ? ?
SING CE1 HE1 ? ?
SING CE2 CZ ? ?
SING CE2 HE2 ? ?
SING CZ HZ ? ?
stop_
save_
save_chem_comp_DLE
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-LEUCINE
_BMRB_code .
_PDB_code DLE
_Standard_residue_derivative .
_Molecular_mass 131.173
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 12:02:43 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD1 CD1 C . 0 . ?
CD2 CD2 C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HG HG H . 0 . ?
HD11 HD11 H . 0 . ?
HD12 HD12 H . 0 . ?
HD13 HD13 H . 0 . ?
HD21 HD21 H . 0 . ?
HD22 HD22 H . 0 . ?
HD23 HD23 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
SING CG CD1 ? ?
SING CG CD2 ? ?
SING CG HG ? ?
SING CD1 HD11 ? ?
SING CD1 HD12 ? ?
SING CD1 HD13 ? ?
SING CD2 HD21 ? ?
SING CD2 HD22 ? ?
SING CD2 HD23 ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_DAL
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-ALANINE
_BMRB_code .
_PDB_code DAL
_Standard_residue_derivative .
_Molecular_mass 89.093
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 12:04:02 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
H2 H2 H . 0 . ?
HA HA H . 0 . ?
HB1 HB1 H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N H ? ?
SING N H2 ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB HB1 ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_DPR
_Saveframe_category polymer_residue
_Mol_type 'D-peptide linking'
_Name_common D-PROLINE
_BMRB_code .
_PDB_code DPR
_Standard_residue_derivative .
_Molecular_mass 115.130
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 12:05:25 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD CD C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
OXT OXT O . 0 . ?
H H H . 0 . ?
HA HA H . 0 . ?
HB2 HB2 H . 0 . ?
HB3 HB3 H . 0 . ?
HG2 HG2 H . 0 . ?
HG3 HG3 H . 0 . ?
HD2 HD2 H . 0 . ?
HD3 HD3 H . 0 . ?
HXT HXT H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N CA ? ?
SING N CD ? ?
SING N H ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB CG ? ?
SING CB HB2 ? ?
SING CB HB3 ? ?
SING CG CD ? ?
SING CG HG2 ? ?
SING CG HG3 ? ?
SING CD HD2 ? ?
SING CD HD3 ? ?
DOUB C O ? ?
SING C OXT ? ?
SING OXT HXT ? ?
stop_
save_
save_chem_comp_NH2
_Saveframe_category polymer_residue
_Mol_type non-polymer
_Name_common 'AMINO GROUP'
_BMRB_code .
_PDB_code NH2
_Standard_residue_derivative .
_Molecular_mass 16.023
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Wed Jul 13 13:32:02 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
N N N . 0 . ?
HN1 HN1 H . 0 . ?
HN2 HN2 H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
SING N HN1 ? ?
SING N HN2 ? ?
stop_
save_
save_chem_comp_LML
_Saveframe_category polymer_residue
_Mol_type non-polymer
_Name_common 'ISOBUTYL MALONIC ACID'
_BMRB_code .
_PDB_code LML
_Standard_residue_derivative .
_Molecular_mass 160.168
_Mol_paramagnetic .
_Details
;
Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 12 12:15:01 2011
;
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
C1 C1 C . 0 . ?
O1 O1 O . 0 . ?
OXT OXT O . 0 . ?
CA CA C . 0 . ?
CB CB C . 0 . ?
CG CG C . 0 . ?
CD1 CD1 C . 0 . ?
CD2 CD2 C . 0 . ?
C C C . 0 . ?
O O O . 0 . ?
O2 O2 O . 0 . ?
HXT HXT H . 0 . ?
HA HA H . 0 . ?
HB1 HB1 H . 0 . ?
HB2 HB2 H . 0 . ?
HG HG H . 0 . ?
HD11 HD11 H . 0 . ?
HD12 HD12 H . 0 . ?
HD13 HD13 H . 0 . ?
HD21 HD21 H . 0 . ?
HD22 HD22 H . 0 . ?
HD23 HD23 H . 0 . ?
HO2 HO2 H . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
DOUB C1 O1 ? ?
SING C1 OXT ? ?
SING C1 CA ? ?
SING OXT HXT ? ?
SING CA CB ? ?
SING CA C ? ?
SING CA HA ? ?
SING CB CG ? ?
SING CB HB1 ? ?
SING CB HB2 ? ?
SING CG CD1 ? ?
SING CG CD2 ? ?
SING CG HG ? ?
SING CD1 HD11 ? ?
SING CD1 HD12 ? ?
SING CD1 HD13 ? ?
SING CD2 HD21 ? ?
SING CD2 HD22 ? ?
SING CD2 HD23 ? ?
DOUB C O ? ?
SING C O2 ? ?
SING O2 HO2 ? ?
stop_
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$A n/a . . . . .
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source
_Saveframe_category experimental_source
loop_
_Mol_label
_Production_method
_Host_organism_name_common
_Genus
_Species
_Strain
_Vector_name
$A 'chemical synthesis' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$A 2.6 mM .
stop_
save_
############################
# Computer software used #
############################
save_DYANA
_Saveframe_category software
_Name DYANA
_Version .
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model DRX
_Field_strength 400
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_COSY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name COSY
_Sample_label $sample_1
save_
save_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name TOCSY
_Sample_label $sample_1
save_
save_NOESY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name NOESY
_Sample_label $sample_1
save_
save_ROESY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name ROESY
_Sample_label $sample_1
save_
#######################
# Sample conditions #
#######################
save_sample_cond_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 5.7 . n/a
pressure 1 . atm
temperature 285 . K
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_ref
_Saveframe_category chemical_shift_reference
_Details .
loop_
_Mol_common_name
_Atom_type
_Atom_isotope_number
_Atom_group
_Chem_shift_units
_Chem_shift_value
_Reference_method
_Reference_type
_External_reference_sample_geometry
_External_reference_location
_External_reference_axis
_Indirect_shift_ratio_citation_label
_Correction_value_citation_label
H2O H 1 protons ppm . internal direct . . . $entry_citation $entry_citation
stop_
save_
###################################
# Assigned chemical shift lists #
###################################
###################################################################
# Chemical Shift Ambiguity Index Value Definitions #
# #
# The values other than 1 are used for those atoms with different #
# chemical shifts that cannot be assigned to stereospecific atoms #
# or to specific residues or chains. #
# #
# Index Value Definition #
# #
# 1 Unique (including isolated methyl protons, #
# geminal atoms, and geminal methyl #
# groups with identical chemical shifts) #
# (e.g. ILE HD11, HD12, HD13 protons) #
# 2 Ambiguity of geminal atoms or geminal methyl #
# proton groups (e.g. ASP HB2 and HB3 #
# protons, LEU CD1 and CD2 carbons, or #
# LEU HD11, HD12, HD13 and HD21, HD22, #
# HD23 methyl protons) #
# 3 Aromatic atoms on opposite sides of #
# symmetrical rings (e.g. TYR HE1 and HE2 #
# protons) #
# 4 Intraresidue ambiguities (e.g. LYS HG and #
# HD protons or TRP HZ2 and HZ3 protons) #
# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) #
# 6 Intermolecular ambiguities (e.g. ASP 31 CA #
# in monomer 1 and ASP 31 CA in monomer 2 #
# of an asymmetrical homodimer, duplex #
# DNA assignments, or other assignments #
# that may apply to atoms in one or more #
# molecule in the molecular assembly) #
# 9 Ambiguous, specific ambiguity not defined #
# #
###################################################################
save_chem_shift_set_1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_cond_1
_Chem_shift_reference_set_label $chemical_shift_ref
_Mol_system_component_name 'retro-inverso peptide'
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 . 1 LML HA H 3.398 0.005 1
2 . 1 LML HB2 H 1.851 0.008 2
3 . 1 LML HB3 H 1.585 0.007 2
4 . 1 LML HG H 1.444 0.008 1
5 . 1 LML HD1 H 0.896 0.005 1
6 . 1 LML HD2 H 0.896 0.005 1
7 . 2 DGN H H 8.766 0.006 1
8 . 2 DGN HA H 4.384 0.008 1
9 . 2 DGN HB2 H 2.395 0.005 2
10 . 2 DGN HB3 H 2.260 0.011 2
11 . 2 DGN HG2 H 1.938 0.007 1
12 . 2 DGN HG3 H 1.938 0.007 1
13 . 3 DAR H H 8.840 0.006 1
14 . 3 DAR HA H 4.209 0.007 1
15 . 3 DAR HB2 H 1.872 0.010 2
16 . 3 DAR HB3 H 1.802 0.007 2
17 . 3 DAR HG2 H 1.666 0.008 1
18 . 3 DAR HG3 H 1.666 0.008 1
19 . 3 DAR HD2 H 3.187 0.006 1
20 . 3 DAR HD3 H 3.187 0.006 1
21 . 3 DAR HE H 7.831 0.005 1
22 . 4 DAL H H 8.221 0.004 1
23 . 4 DAL HA H 4.281 0.001 1
24 . 4 DAL HB H 1.373 0.004 1
25 . 5 DVA H H 8.135 0.006 1
26 . 5 DVA HA H 4.052 0.007 1
27 . 5 DVA HB H 2.040 0.012 1
28 . 5 DVA HG1 H 0.955 0.005 1
29 . 5 DVA HG2 H 0.918 0.014 1
30 . 6 DAR H H 8.551 0.006 1
31 . 6 DAR HA H 4.643 0.007 1
32 . 6 DAR HB2 H 1.841 0.008 1
33 . 6 DAR HB3 H 1.841 0.008 1
34 . 6 DAR HG2 H 1.729 0.005 2
35 . 6 DAR HG3 H 1.666 0.005 2
36 . 6 DAR HD2 H 3.208 0.007 1
37 . 6 DAR HD3 H 3.208 0.007 1
38 . 6 DAR HE H 7.256 0.005 1
39 . 7 DPR HA H 4.382 0.005 1
40 . 7 DPR HB2 H 2.307 0.015 2
41 . 7 DPR HB3 H 1.885 0.008 2
42 . 7 DPR HG2 H 2.018 0.008 1
43 . 7 DPR HG3 H 2.018 0.008 1
44 . 7 DPR HD2 H 3.838 0.008 2
45 . 7 DPR HD3 H 3.639 0.009 2
46 . 8 DAL H H 8.573 0.004 1
47 . 8 DAL HA H 4.281 0.002 1
48 . 8 DAL HB H 1.389 0.006 1
49 . 9 DLE H H 8.448 0.005 1
50 . 9 DLE HA H 4.380 0.005 1
51 . 9 DLE HB2 H 1.676 0.015 1
52 . 9 DLE HB3 H 1.676 0.015 1
53 . 9 DLE HG H 1.635 0.005 1
54 . 9 DLE HD1 H 0.926 0.005 1
55 . 9 DLE HD2 H 0.873 0.008 1
56 . 10 DSN H H 8.442 0.014 1
57 . 10 DSN HA H 4.429 0.012 1
58 . 10 DSN HB2 H 3.949 0.017 2
59 . 10 DSN HB3 H 3.868 0.012 2
60 . 10 DSN HG H 1.454 0.000 1
61 . 11 GLY H H 8.539 0.006 1
62 . 11 GLY HA2 H 3.933 0.002 1
63 . 11 GLY HA3 H 3.933 0.002 1
64 . 12 DPN H H 8.306 0.006 1
65 . 12 DPN HA H 4.604 0.007 1
66 . 12 DPN HB2 H 3.114 0.013 2
67 . 12 DPN HB3 H 3.049 0.008 2
68 . 12 DPN HD1 H 7.259 0.003 1
69 . 12 DPN HE1 H 7.359 0.003 1
70 . 12 DPN HE2 H 7.359 0.003 1
71 . 12 DPN HD2 H 7.259 0.003 1
72 . 13 DAS H H 8.396 0.006 1
73 . 13 DAS HA H 4.529 0.008 1
74 . 13 DAS HB2 H 2.672 0.003 1
75 . 13 DAS HB3 H 2.672 0.003 1
76 . 14 GLY H H 7.954 0.007 1
77 . 14 GLY HA2 H 3.906 0.000 2
78 . 14 GLY HA3 H 3.837 0.001 2
79 . 15 DAR H H 8.128 0.003 1
80 . 15 DAR HA H 4.334 0.007 1
81 . 15 DAR HB2 H 1.830 0.008 1
82 . 15 DAR HB3 H 1.830 0.008 1
83 . 15 DAR HG2 H 1.605 0.007 1
84 . 15 DAR HG3 H 1.605 0.007 1
85 . 15 DAR HD2 H 3.179 0.009 1
86 . 15 DAR HD3 H 3.179 0.009 1
87 . 15 DAR HE H 7.412 0.006 1
88 . 16 DVA H H 8.358 0.006 1
89 . 16 DVA HA H 4.102 0.004 1
90 . 16 DVA HB H 2.086 0.014 1
91 . 16 DVA HG1 H 0.983 0.001 1
92 . 16 DVA HG2 H 0.961 0.010 1
93 . 17 GLY H H 8.693 0.006 1
94 . 17 GLY HA2 H 4.049 0.012 2
95 . 17 GLY HA3 H 3.978 0.002 2
96 . 18 DSN H H 8.453 0.005 1
97 . 18 DSN HA H 4.415 0.010 1
98 . 18 DSN HB2 H 3.929 0.001 2
99 . 18 DSN HB3 H 3.875 0.006 2
100 . 19 GLY H H 8.670 0.006 1
101 . 19 GLY HA2 H 3.923 0.012 1
102 . 19 GLY HA3 H 3.923 0.012 1
stop_
save_