1JPK Lyase date Aug 02, 2001
title Gly156asp Mutant Of Human Urod, Human Uroporphyrinogen III Decarboxylase
authors J.D.Phillips, T.L.Parker, H.L.Schubert, F.G.Whitby, C.P.Hill, J.P.Kushner
compound source
Molecule: Uroporphyrinogen Decarboxylase
Chain: A
Synonym: Urod, Upd, Uro'Gen III Decarboxylase
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Urod
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon +
Expression_system_plasmid: Pet14b
symmetry Space Group: P 31 2 1
R_factor 0.195 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
103.200 103.200 73.620 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1JPH, 1JPI
  • uroporphyrinogen decarboxyla...

  • Primary referenceFunctional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase., Phillips JD, Parker TL, Schubert HL, Whitby FG, Hill CP, Kushner JP, Blood 2001 Dec 1;98(12):3179-85. PMID:11719352
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (1jpk.pdb1.gz) 124 Kb
  • CSU: Contacts of Structural Units for 1JPK
  • Likely Quarternary Molecular Structure file(s) for 1JPK
  • Structure Factors (168 Kb)
  • Retrieve 1JPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JPK from S2C, [Save to disk]
  • Re-refined 1jpk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JPK 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 1JPK
  • 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 1JPK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jpka_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1jpk 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: [1jpk] [1jpk_A]
  • SWISS-PROT database: [P06132]
  • Domain organization of [DCUP_HUMAN] by SWISSPFAM
  • Other resources with information on 1JPK
  • Community annotation for 1JPK 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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