7E9V | pdb_00007e9v

The Crystal Structure of human UMP-CMP kinase from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb7E9V/pdb

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


• Deposited: 2021-03-05 Released: 2021-03-24 
• Deposition Author(s): Wang, F., Lin, D., Wang, R., Wei, X., Shen, Z., Wang, M.
• Funding Organization(s): The Natural Science Foundation of Jiangsu Province

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of human UMP-CMP kinase from Biortus.

Wang, F., Lin, D., Wang, R., Wei, X., Shen, Z., Wang, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.45 kDa 
• Atom Count: 1,565 
• Modeled Residue Count: 192 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UMP-CMP kinase	A	214	Homo sapiens	Mutation(s): 0  Gene Names: CMPK1, CMK, CMPK, UCK, UMK, UMPK EC: 2.7.4.14 (PDB Primary Data), 2.7.4.6 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P30085 (Homo sapiens) Explore P30085  Go to UniProtKB:  P30085
PHAROS:  P30085 GTEx:  ENSG00000162368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.926	α = 90
b = 61.926	β = 90
c = 225.397	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Wang, F., Lin, D., Wang, R., Wei, X., Shen, Z., Wang, M.

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Funding Organization	Location	Grant Number
The Natural Science Foundation of Jiangsu Province	China	BK20170222

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description