BMRB Entry 7434

Name: Backbone assignment of 3F5 heavy chain antibody fragment in its free form and in complex with PABPN1
Published: 2009-11-24

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR7434

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone assignment of 3F5 heavy chain antibody fragment in its free form and in complex with PABPN1

Deposition date:

2009-10-27

Original release date:

2009-11-24

Authors:

Impagliazzo, Antonietta; Ubbink, Marcellus

Citation:

Citation: Impagliazzo, Antonietta; Tepper, Armand; Verrips, Theo; Ubbink, Marcellus; van der Maarel, Silvere. "Structural insight into the recognition of PABPN1 by the flexible loops of a heavy chain antibody fragment" .

Assembly members:

Assembly members:
3F5_VHH, polymer, 136 residues, Formula weight is not available
PABPN1pept, polymer, 32 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Lama glama Taxonomy ID: 9844 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Lama glama

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pet28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
3F5_VHH: MAEVQLVESGGGLVQAGGSL RLSCAASGRTFSGYGMGWFR QAPGKEREFVAAISWRGGNT YYADSVKGRFTISRDNAKNT VWLQMNSLKPEDTAVYYCSG FVRTRDDPSRIRNYWGQGTQ VTVSTAAALEHHHHHH
PABPN1pept: AIEDPELEAIKARVREMEEE AEKLKELQNEVK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	228
15N chemical shifts	115
1H chemical shifts	116

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	3F5	1
2	PABPN1pept	2

Entities:

Entity 1, 3F5 136 residues - Formula weight is not available

1

MET

ALA

GLU

VAL

GLN

LEU

VAL

GLU

SER

GLY

2

GLY

LEU

VAL

GLN

ALA

GLY

SER

LEU

3

ARG

LEU

SER

CYS

ALA

SER

GLY

ARG

THR

4

PHE

SER

GLY

TYR

GLY

MET

GLY

TRP

PHE

ARG

5

GLN

ALA

PRO

GLY

LYS

GLU

ARG

GLU

PHE

VAL

6

ALA

ILE

SER

TRP

ARG

GLY

ASN

THR

7

TYR

ALA

ASP

SER

VAL

LYS

GLY

ARG

PHE

8

THR

ILE

SER

ARG

ASP

ASN

ALA

LYS

ASN

THR

9

VAL

TRP

LEU

GLN

MET

ASN

SER

LEU

LYS

PRO

10

GLU

ASP

THR

ALA

VAL

TYR

CYS

SER

GLY

11

PHE

VAL

ARG

THR

ARG

ASP

PRO

SER

ARG

12

ILE

ARG

ASN

TYR

TRP

GLY

GLN

GLY

THR

GLN

13

VAL

THR

VAL

SER

THR

ALA

LEU

GLU

14

HIS

Entity 2, PABPN1pept 32 residues - Formula weight is not available

1

ALA

ILE

GLU

ASP

PRO

GLU

LEU

GLU

ALA

ILE

2

LYS

ALA

ARG

VAL

ARG

GLU

MET

GLU

3

ALA

GLU

LYS

LEU

LYS

GLU

LEU

GLN

ASN

GLU

4

VAL

LYS

Samples:

sample_1: 3F5 VHH, [U-98% 15N], 1.6 mM; PABPN1 pept, [U-98% 15N], 1.6 mM; H2O 90%; D2O 10%; NaCl 150 mM

sample_2: 3F5 VHH, [U-98% 13C; U-98% 15N], 1.6 mM; PABPN1 pept, [U-98% 13C; U-98% 15N], 1.6 mM; H2O 90%; D2O 10%; NaCl 150 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1

Software:

ANSIG, Kraulis - chemical shift assignment

NMR spectrometers:

Bruker DMX 600 MHz