1JXV | pdb_00001jxv

Crystal Structure of Human Nucleoside Diphosphate Kinase A

PDB DOI: https://doi.org/10.2210/pdb1JXV/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2001-09-10 Released: 2002-04-10
Deposition Author(s): Min, K., Song, H.K., Chang, C., Kim, S.Y., Lee, K.J., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.263 (Depositor), 0.225 (DCC)
R-Value Work:
0.207 (Depositor), 0.224 (DCC)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor.

Min, K., Song, H.K., Chang, C., Kim, S.Y., Lee, K.J., Suh, S.W.

(2002) Proteins 46: 340-342

PubMed: 11835509 Search on PubMed
DOI: https://doi.org/10.1002/prot.10038
Primary Citation Related Structures:
1JXV

Organizational Affiliation

School of Chemistry and Molecular Engineering, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 103.02 kDa
Atom Count: 7,295
Modeled Residue Count: 894
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside Diphosphate Kinase A	A, B, C, D, E A, B, C, D, E, F	152	Homo sapiens	Mutation(s): 0 Gene Names: nm23-H1 EC: 2.7.4.6 (PDB Primary Data), 3.1.24 (UniProt), 2.7.4.18 (UniProt), 2.7.11.1 (UniProt), 2.7.13.3 (UniProt), 3.1.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15531 (Homo sapiens) Explore P15531 Go to UniProtKB: P15531
PHAROS: P15531 GTEx: ENSG00000239672
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15531
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.263 (Depositor), 0.225 (DCC)
R-Value Work: 0.207 (Depositor), 0.224 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.21	α = 90
b = 78.11	β = 101.33
c = 82.29	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-04-10
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.