1PDA Transferase date Nov 17, 1992
title Structure Of Porphobilinogen Deaminase Reveals A Flexible Mu Polymerase With A Single Catalytic Site
authors G.V.Louie, P.D.Brownlie, R.Lambert, J.B.Cooper, T.L.Blundell, S.P M.J.Warren, S.C.Woodcock, P.M.Jordan
compound source
Molecule: Porphobilinogen Deaminase
Chain: A
Ec: 2.5.1.61
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.188 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.000 75.900 50.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.76 Å
ligand ACY, DPM enzyme Transferase E.C.2.5.1.61 BRENDA
related structures by homologous chain: 1GTK, 2YPN
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site., Louie GV, Brownlie PD, Lambert R, Cooper JB, Blundell TL, Wood SP, Warren MJ, Woodcock SC, Jordan PM, Nature 1992 Sep 3;359(6390):33-9. PMID:1522882
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (1pda.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1PDA
  • CSU: Contacts of Structural Units for 1PDA
  • Likely Quarternary Molecular Structure file(s) for 1PDA
  • Structure Factors (378 Kb)
  • Retrieve 1PDA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PDA from S2C, [Save to disk]
  • Re-refined 1pda structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1PDA 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 1PDA
  • 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
  • 3D motif for 1PDA, from MSDmotif at EBI
  • Genome occurence of 1PDA's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pda_2, region 220-307 [Jmol] [rasmolscript] [script source]
        - Domain d1pda_1, region 3-219 [Jmol] [rasmolscript] [script source]
  • 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: [1pda] [1pda_A]
  • SWISS-PROT database: [P06983]
  • Domain organization of [HEM3_ECOLI] by SWISSPFAM
    • Other resources with information on 1PDA
  • Community annotation for 1PDA 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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