1PDV Protein Binding date May 20, 2003
title Crystal Structure Of Human Dj-1, P 31 2 1 Space Group
authors X.Tao, L.Tong
compound source
Molecule: Dj-1
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.190 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.658 75.658 75.488 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand MSE enzyme
related structures by homologous chain: 1PE0, 1UCF
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of human DJ-1, a protein associated with early onset Parkinson's disease., Tao X, Tong L, J Biol Chem 2003 Aug 15;278(33):31372-9. PMID:12761214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (1pdv.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 1PDV
  • CSU: Contacts of Structural Units for 1PDV
  • Likely Quarternary Molecular Structure file(s) for 1PDV
  • Structure Factors (383 Kb)
  • Retrieve 1PDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PDV from S2C, [Save to disk]
  • Re-refined 1pdv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PDV 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 1PDV
  • 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 1PDV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pdva_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1pdv 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: [1pdv] [1pdv_A]
  • SWISS-PROT database: [Q99497]
  • Domain organization of [PARK7_HUMAN] by SWISSPFAM
  • Other resources with information on 1PDV
  • Community annotation for 1PDV 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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