BMRB Entry 10098

Name: Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta
Published: 2008-08-15

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PDB ID: 1r79
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10098
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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:

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

Deposition date:

2007-02-13

Original release date:

2008-08-15

Authors:

Miyamoto, K.; Tomizawa, T.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Miyamoto, K.; Tomizawa, T.; Koshiba, S.; Inoue, M.; Kigawa, T.; Yokoyama, S.. "Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta" .

Assembly members:

Assembly members:
C1 Domain, polymer, 84 residues, Formula weight is not available
ZN, non-polymer, 65.409 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: cell free synthesis Vector: P030128-49

Entity Sequences (FASTA):

Entity Sequences (FASTA):
C1 Domain: GSSGSSGTTLASIGKDIIED ADGIAMPHQWLEGNLPVSAK CTVCDKTCGSVLRLQDWRCL WCKAMVHTSCKESLLTKCSG PSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	318
15N chemical shifts	75
1H chemical shifts	506

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Diacylglycerol kinase, delta	1
2	ZINC (II) ION, 1	2
3	ZINC (II) ION, 2	2

Entities:

Entity 1, Diacylglycerol kinase, delta 84 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

THR

LEU

2

ALA

SER

ILE

GLY

LYS

ASP

ILE

GLU

ASP

3

ALA

ASP

GLY

ILE

ALA

MET

PRO

HIS

GLN

TRP

4

LEU

GLU

GLY

ASN

LEU

PRO

VAL

SER

ALA

LYS

5

CYS

THR

VAL

CYS

ASP

LYS

THR

CYS

GLY

SER

6

VAL

LEU

ARG

LEU

GLN

ASP

TRP

ARG

CYS

LEU

7

TRP

CYS

LYS

ALA

MET

VAL

HIS

THR

SER

CYS

8

LYS

GLU

SER

LEU

THR

LYS

CYS

SER

GLY

9

PRO

SER

GLY

Entity 2, ZINC (II) ION, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: C1 Domain, [U-13C; U-15N], 1.05 mM; d-Tris-HCl 20 mM; NaCl 100 mM; NaN3 0.02%; ZnCl2 100 uM; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	not available	condition_1
3D 15N-separated NOESY	sample_1	not available	condition_1

Software:

xwinnmr v2.6, Bruker - collection

NMRPipe v20020425, Delaglio, F. - processing

NMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.863, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, P - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz

PDB	1R79
DBJ	BAA09766 BAA11134 BAC11809 BAE02082
GB	AAY24321 EAW71047 EAW71048 EAW71049 EAW71050
REF	NP_003639 NP_690618 XP_001114920 XP_001916296 XP_002918009
SP	Q16760
AlphaFold	Q16760