5DOT Ligase date Sep 11, 2015
title Crystal Structure Of Human Carbamoyl Phosphate Synthetase I Apo Form
authors L.M.Polo, S.De Cima, I.Fita, V.Rubio
compound source
Molecule: Carbamoyl-Phosphate Synthase [Ammonia], Mitochond
Chain: A, B
Fragment: Mature Enzyme
Synonym: Carbamoyl-Phosphate Synthetase I,Cpsase I
Ec: 6.3.4.16
Engineered: Yes
Other_details: Mature Cps1 With N-Terminal His-Tag For Puri Purposes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Gene: Cps1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac-Bmon14272
symmetry Space Group: P 1 21 1
R_factor 0.165 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.337 133.482 142.907 90.00 102.51 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand EDO, GOL, NI enzyme Ligase E.C.6.3.4.16 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • endopeptidase activity


  • Primary referenceStructure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis., de Cima S, Polo LM, Diez-Fernandez C, Martinez AI, Cervera J, Fita I, Rubio V, Sci Rep. 2015 Nov 23;5:16950. doi: 10.1038/srep16950. PMID:26592762
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (866 Kb) [Save to disk]
  • Biological Unit Coordinates (5dot.pdb1.gz) 856 Kb
  • LPC: Ligand-Protein Contacts for 5DOT
  • CSU: Contacts of Structural Units for 5DOT
  • Structure Factors (7536 Kb)
  • Retrieve 5DOT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DOT from S2C, [Save to disk]
  • Re-refined 5dot structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DOT 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 5DOT
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dot_B] [5dot_A] [5dot]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DOT: [CPSase_L_D3] [CPSase_sm_chain] [MGS ] by SMART
  • Other resources with information on 5DOT
  • Community annotation for 5DOT at PDBWiki (http://pdbwiki.org)

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