2YVQ Ligase date Apr 13, 2007
title Crystal Structure Of Mgs Domain Of Carbamoyl-Phosphate Synthetase From Homo Sapiens
authors Y.Xie, Ihsanawati, S.Kishishita, K.Murayama, C.Takemoto, M.Shirozu, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Carbamoyl-Phosphate Synthase
Chain: A
Fragment: Mgs Domain
Synonym: Carbamoyl-Phosphate Synthetase I, Cpsase I
Ec: 6.3.4.16
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pk060110-54-Md01
Other_details: Cell-Free Protein Synthesis
symmetry Space Group: P 32 2 1
R_factor 0.232 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.505 50.505 97.634 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.98 Å
ligand
enzyme Ligase E.C.6.3.4.16 BRENDA
note 2YVQ is a representative structure
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (2yvq.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (2yvq.pdb2.gz) 46 Kb
  • CSU: Contacts of Structural Units for 2YVQ
  • Likely Quarternary Molecular Structure file(s) for 2YVQ
  • Structure Factors (86 Kb)
  • Retrieve 2YVQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YVQ from S2C, [Save to disk]
  • Re-refined 2yvq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YVQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2YVQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2YVQ, from MSDmotif at EBI
  • Fold representative 2yvq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yvq_A] [2yvq]
  • SWISS-PROT database: [P31327]
  • Domain organization of [CPSM_HUMAN] by SWISSPFAM
  • Domain found in 2YVQ: [MGS ] by SMART
  • Other resources with information on 2YVQ
  • Community annotation for 2YVQ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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