1C9Y Transferase date Aug 03, 1999
title Human Ornithine Transcarbamylase: Crystallographic Insights Substrate Recognition And Catalytic Mechanism
authors D.Shi, X.Yu, H.Morizono, M.Tuchman, N.M.Allewell
compound source
Molecule: Ornithine Carbamoyltransferase
Chain: A
Synonym: Otcase, Ornithine Transcarbamylase
Ec: 2.1.3.3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_vector: Petotcii
symmetry Space Group: P 21 3
R_factor 0.187 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.410 125.410 125.410 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CP, NVA enzyme Transferase E.C.2.1.3.3 BRENDA
related structures by homologous chain: 1EP9, 1OTH
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate and L-norvaline at 1.9 A resolution., Shi D, Morizono H, Aoyagi M, Tuchman M, Allewell NM, Proteins 2000 Jun 1;39(4):271-7. PMID:10813810
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (1c9y.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 1C9Y
  • CSU: Contacts of Structural Units for 1C9Y
  • Likely Quarternary Molecular Structure file(s) for 1C9Y
  • Structure Factors (374 Kb)
  • Retrieve 1C9Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1C9Y from S2C, [Save to disk]
  • Re-refined 1c9y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1C9Y 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 1C9Y
  • 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 1C9Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1c9ya2, region A:185-354 [Jmol] [rasmolscript] [script source]
        - Domain d1c9ya1, region A:34-184 [Jmol] [rasmolscript] [script source]
  • Fold representative 1c9y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1c9y] [1c9y_A]
  • SWISS-PROT database: [P00480]
  • Domain organization of [OTC_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1C9Y with the sequences similar proteins can be viewed for 1C9Y's classification [OTC_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [OTC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1C9Y
  • Community annotation for 1C9Y 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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