1PKH Hydrolase date Jun 05, 2003
title Structural Basis For Recognition And Catalysis By The Bifunc Dctp Deaminase And Dutpase From Methanococcus Jannaschii
authors J.L.Huffman, H.Li, R.H.White, J.A.Tainer
compound source
Molecule: Bifunctional Deaminasediphosphatase
Chain: A, B
Synonym: Mjdcd-Dut, Dcddut
Ec: 3.5.4.13, 3.6.1.23
Engineered: Yes
Organism_scientific: Methanocaldococcus Jannaschii
Organism_taxid: 2190
Gene: Mj0430
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet17b
symmetry Space Group: P 21 3
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.700 110.700 110.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.42 Å
ligand EDO enzyme Hydrolase E.C.3.5.4.13 BRENDA
related structures by homologous chain: 1PKK
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii., Huffman JL, Li H, White RH, Tainer JA, J Mol Biol 2003 Aug 22;331(4):885-96. PMID:12909016
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (1pkh.pdb1.gz) 194 Kb
  • Biological Unit Coordinates (1pkh.pdb2.gz) 34 Kb
  • Biological Unit Coordinates (1pkh.pdb3.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 1PKH
  • CSU: Contacts of Structural Units for 1PKH
  • Likely Quarternary Molecular Structure file(s) for 1PKH
  • Structure Factors (772 Kb)
  • Retrieve 1PKH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PKH from S2C, [Save to disk]
  • Re-refined 1pkh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PKH 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 1PKH
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1PKH 1PKHA 1PKHB from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1PKH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pkha_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pkhb_, region B [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: [1pkh] [1pkh_A] [1pkh_B]
  • SWISS-PROT database: [Q57872]
  • Domain organization of [DCD_METJA] by SWISSPFAM
  • Other resources with information on 1PKH
  • Community annotation for 1PKH 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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