1ZS6

structure of human nucleoside-diphosphate kinase 3

PDB DOI: https://doi.org/10.2210/pdb1ZS6/pdb

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

Deposited: 2005-05-23 Released: 2005-06-07
Deposition Author(s): Choe, J., Dimov, S., Arrowsmith, C., Edwards, A., Sundstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.255
R-Value Work: 0.211
R-Value Observed: 0.213

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of human nucleoside-diphosphate kinase 3

Dimov, S., Choe, J., ARROWSMITH, C., EDWARDS, A., SUNDSTROM, M., BOCHKAREV, A., PARK, H.

To be published.

Macromolecule Content

Total Structure Weight: 58.4 kDa
Atom Count: 3,773
Modelled Residue Count: 456
Deposited Residue Count: 507
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase 3	A, B, C [auth D]	169	Homo sapiens	Mutation(s): 0 Gene Names: NME3 EC: 2.7.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q13232 (Homo sapiens) Explore Q13232 Go to UniProtKB: Q13232
PHAROS: Q13232 GTEx: ENSG00000103024
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13232
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth D] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth D] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth D]	D [auth A], E [auth B], F [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.255
R-Value Work: 0.211
R-Value Observed: 0.213
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.614	α = 90
b = 86.614	β = 90
c = 126.856	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-06-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-06-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

1ZS6

structure of human nucleoside-diphosphate kinase 3

Structure of human nucleoside-diphosphate kinase 3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)