2YVQ | pdb_00002yvq

Crystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens

• PDB DOI: https://doi.org/10.2210/pdb2YVQ/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-04-13 Released: 2008-04-15 
• Deposition Author(s): Xie, Y., Ihsanawati, Kishishita, S., Murayama, K., Takemoto, C., Shirozu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens

Xie, Y., Ihsanawati, Kishishita, S., Murayama, K., Takemoto, C., Shirozu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.61 kDa 
• Atom Count: 1,124 
• Modeled Residue Count: 134 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyl-phosphate synthase	A	143	Homo sapiens	Mutation(s): 0  EC: 6.3.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P31327 (Homo sapiens) Explore P31327  Go to UniProtKB:  P31327
PHAROS:  P31327 GTEx:  ENSG00000021826

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.505	α = 90
b = 50.505	β = 90
c = 97.634	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Xie, Y., Ihsanawati, Kishishita, S., Murayama, K., Takemoto, C., Shirozu, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references