3L7U | pdb_00003l7u

Crystal structure of human NM23-H1

• PDB DOI: https://doi.org/10.2210/pdb3L7U/pdb

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


• Deposited: 2009-12-29 Released: 2010-11-10 
• Deposition Author(s): Han, B.G., Min, K., Lee, B.I., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Refined Structure of Human NM23-H1 from a Hexagonal Crystal

Han, B.G., Min, K., Lee, B.I., Lee, S.

(2010) Bull Korean Chem Soc 31: 1397-1399

• DOI: https://doi.org/10.5012/bkcs.2010.31.5.1397

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.22 kDa 
• Atom Count: 3,936 
• Modeled Residue Count: 458 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase A	A, B, C	172	Homo sapiens	Mutation(s): 0  Gene Names: NME1, NDPKA, NM23 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth B], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.51	α = 90
b = 154.51	β = 90
c = 111.821	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Han, B.G., Min, K., Lee, B.I., Lee, S.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description