3CH4

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.221
R-Value Work: 0.199
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22151
Primary Citation of Related Structures:
3CH4

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15126
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	D [auth B], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B SDF format, chain C [auth B] MOL2 format, chain B MOL2 format, chain C [auth B]	B, C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B Focus chain C [auth B] Interactions & Density Focus chain B Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.221
R-Value Work: 0.199
R-Value Observed: 0.199
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

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Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3CH4

The Crystal Structure of Human Phosphomavelonate Kinase At 1.8 A Resolution

Crystal structure of human phosphomavelonate kinase at 1.8 A resolution

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)