BMRB Entry 11088

Name: Solution structure of the PH domain of Dynamin-2 from human
Published: 2011-01-19

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PDB ID: 2ys1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11088
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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 PH domain of Dynamin-2 from human

Deposition date:

2010-01-18

Original release date:

2011-01-19

Authors:

Li, H.; Sato, M.; Tochio, N.; Koshiba, S.; Watanabe, S.; Harada, T.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Li, H.; Sato, M.; Tochio, N.; Koshiba, S.; Watanabe, S.; Harada, T.; Kigawa, T.; Yokoyama, S.. "Solution structure of the PH domain of Dynamin-2 from human" .

Assembly members:

Assembly members:
PH domain, polymer, 113 residues, Formula weight is not available

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 Host organism: E. coli - cell free Vector: P060904-04

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PH domain: GSSGSSGVIRRGWLTINNIS LMKGGSKEYWFVLTAESLSW YKDEEEKEKKYMLPLDNLKI RDVEKGFMSNKHVFAIFNTE QRNVYKDLRQIELACDSQED VDSWKASFLRAGV

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	494
15N chemical shifts	113
1H chemical shifts	789

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PH domain	1

Entities:

Entity 1, PH domain 113 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

VAL

ILE

ARG

2

ARG

GLY

TRP

LEU

THR

ILE

ASN

ILE

SER

3

LEU

MET

LYS

GLY

SER

LYS

GLU

TYR

TRP

4

PHE

VAL

LEU

THR

ALA

GLU

SER

LEU

SER

TRP

5

TYR

LYS

ASP

GLU

LYS

GLU

LYS

6

TYR

MET

LEU

PRO

LEU

ASP

ASN

LEU

LYS

ILE

7

ARG

ASP

VAL

GLU

LYS

GLY

PHE

MET

SER

ASN

8

LYS

HIS

VAL

PHE

ALA

ILE

PHE

ASN

THR

GLU

9

GLN

ARG

ASN

VAL

TYR

LYS

ASP

LEU

ARG

GLN

10

ILE

GLU

LEU

ALA

CYS

ASP

SER

GLN

GLU

ASP

11

VAL

ASP

SER

TRP

LYS

ALA

SER

PHE

LEU

ARG

12

ALA

GLY

VAL

Samples:

sample_1: PH domain, [U-13C; U-15N], 1.17 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	isotropic	condition_1
3D 13N-separated NOESY	sample_1	isotropic	condition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20031121, Delaglio, F. - processing

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

Kujira v0.9820, Kobayashi, N. - data analysis

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

NMR spectrometers:

Bruker AVANCE 800 MHz

PDB	2YS1
DBJ	BAB23745 BAC05190 BAC85978 BAC86481 BAC86797
GB	AAA16746 AAA19736 AAA40523 AAA88025 AAD23603
REF	NP_001005360 NP_001005361 NP_001005362 NP_001034609 NP_001092839
SP	A6H7I5 P39052 P39054 P50570
TPG	DAA27924
AlphaFold	A6H7I5 P39052 P39054 P50570