3CH4 | pdb_00003ch4

The Crystal Structure of Human Phosphomavelonate Kinase At 1.8 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3CH4/pdb

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


• Deposited: 2008-03-07 Released: 2008-07-29 
• Deposition Author(s): Liang, D.-C., Chang, Q., Yan, X.-X., Gu, S.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.221 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of human phosphomavelonate kinase at 1.8 A resolution

Chang, Q., Yan, X.-X., Gu, S.-Y., Liu, J.-F., Liang, D.-C.

(2008) Proteins 73: 254-258

• PubMed: 18618710 
• DOI: https://doi.org/10.1002/prot.22151
• Primary Citation Related Structures: 
  3CH4

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.67 kDa 
• Atom Count: 1,689 
• Modeled Residue Count: 188 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomevalonate kinase	A [auth B]	202	Homo sapiens	Mutation(s): 0  EC: 2.7.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15126 (Homo sapiens) Explore Q15126  Go to UniProtKB:  Q15126
PHAROS:  Q15126 GTEx:  ENSG00000163344

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth B], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	B, C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.221 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.14	α = 90
b = 32.625	β = 111.01
c = 61.786	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Liang, D.-C., Chang, Q., Yan, X.-X., Gu, S.-Y.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations