7KPF

NME2 bound to myristoyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb7KPF/pdb

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


• Deposited: 2020-11-11 Released: 2022-02-02 
• Deposition Author(s): Price, I.R., Lin, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.229 
• R-Value Work: 0.190 

Literature

A Chemical Proteomic Approach reveals the regulation of NME1/2 and cancer metastasis by Long-Chain Fatty Acyl Coenzyme A

Zhang, S., Nelson, O.D., Price, I.R., Zhu, C., Fernandez, I.R., Lu, X., Weiss, R.S., Lin, H.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.14 kDa 
• Atom Count: 7,326 
• Modelled Residue Count: 874 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase B	A, B, C, D, E, F	152	Homo sapiens	Mutation(s): 0  Gene Names: NME2, NM23B EC: 2.7.4.6 (PDB Primary Data), 2.7.13.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P22392 (Homo sapiens) Explore P22392  Go to UniProtKB:  P22392
PHAROS:  P22392 GTEx:  ENSG00000243678

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA (Subject of Investigation/LOI)	G [auth A], H [auth B], J [auth C]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
GOL	L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	I [auth B], K [auth C], M [auth D], N [auth E], O [auth F], P [auth F], Q [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.229 
• R-Value Work: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.727	α = 90
b = 107.515	β = 90
c = 115.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Price, I.R., Lin, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM086703-07

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 2.0: 2023-10-18
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary