1R3Q Lyase date Oct 03, 2003
title Uroporphyrinogen Decarboxylase In Complex With Coproporphyri
authors J.D.Phillips, F.G.Whitby, J.P.Kushner, C.P.Hill
compound source
Molecule: Uroporphyrinogen Decarboxylase
Chain: A
Synonym: Uro-D; Upd
Ec: 4.1.1.37
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
symmetry Space Group: P 31 2 1
R_factor 0.167 R_Free 0.192
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.930 102.930 74.510 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand 1CP, CO2 enzyme Lyase E.C.4.1.1.37 BRENDA
related structures by homologous chain: 1R3T, 1R3W
Gene
Ontology
ChainFunctionProcessComponent
A
  • uroporphyrinogen decarboxyla...


  • Primary referenceStructural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase., Phillips JD, Whitby FG, Kushner JP, Hill CP, EMBO J 2003 Dec 1;22(23):6225-33. PMID:14633982
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (1r3q.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 1R3Q
  • CSU: Contacts of Structural Units for 1R3Q
  • Likely Quarternary Molecular Structure file(s) for 1R3Q
  • Structure Factors (655 Kb)
  • Retrieve 1R3Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R3Q from S2C, [Save to disk]
  • Re-refined 1r3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R3Q 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 1R3Q
  • 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 1R3Q, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r3qa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1r3q 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: [1r3q_A] [1r3q]
  • SWISS-PROT database: [P06132]
  • Domain organization of [DCUP_HUMAN] by SWISSPFAM
  • Other resources with information on 1R3Q
  • Community annotation for 1R3Q 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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