BMRB Entry 25801

Name: UBL domain of the human DNA damage-inducible protein homolog 2
Published: 2016-07-13

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PDB ID: 2n7d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25801
MolProbity Validation Chart

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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:

UBL domain of the human DNA damage-inducible protein homolog 2

Deposition date:

2015-09-08

Original release date:

2016-07-13

Authors:

Siva, Monika; Grantz Saskova, Klara; Veverka, Vaclav

Citation:

Citation: Siva, Monika; Svoboda, Michal; Veverka, Vaclav; Trempe, Jean-Francois; Hofmann, Kay; Kozisek, Milan; Hexnerova, Rozalie; Sedlak, Frantisek; Belza, Jan; Brynda, Jiri; Sacha, Pavel; Hubalek, Martin; Starkova, Jana; Flaisigova, Iva; Konvalinka, Jan; Saskova, Klara Grantz. "Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog" Sci. Rep. 6, 30443-30443 (2016).
PubMed: 27461074

Assembly members:

Assembly members:
entity, polymer, 97 residues, 11142.557 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: n/a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MGHHHHHHHHHHSSGHIEGR HMLLTVYCVRRDLSEVTFSL QVDADFELHNFRALCELESG IPAAESQIVYAERPLTDNHR SLASYGLKDGDVVILRQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	332
15N chemical shifts	83
1H chemical shifts	579

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 97 residues - 11142.557 Da.

1

MET

GLY

HIS

2

HIS

SER

GLY

HIS

ILE

GLU

GLY

ARG

3

HIS

MET

LEU

THR

VAL

TYR

CYS

VAL

ARG

4

ARG

ASP

LEU

SER

GLU

VAL

THR

PHE

SER

LEU

5

GLN

VAL

ASP

ALA

ASP

PHE

GLU

LEU

HIS

ASN

6

PHE

ARG

ALA

LEU

CYS

GLU

LEU

GLU

SER

GLY

7

ILE

PRO

ALA

GLU

SER

GLN

ILE

VAL

TYR

8

ALA

GLU

ARG

PRO

LEU

THR

ASP

ASN

HIS

ARG

9

SER

LEU

ALA

SER

TYR

GLY

LEU

LYS

ASP

GLY

10

ASP

VAL

ILE

LEU

ARG

GLN

Samples:

sample_1: sodium phosphate 25 mM; sodium chloride 100 mM; entity, [U-13C; U-15N], 0.4 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1

Software:

YASARA, YASARA - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - refinement

NMR spectrometers:

Bruker Avance 850 MHz
Bruker Avance 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks