1YKN Oxidoreductase date Jan 18, 2005
title Protocatechuate 3,4-Dioxygenase Y408e Mutant Bound To Dhb
authors C.K.Brown, D.H.Ohlendorf
compound source
Molecule: Protocatechuate 3,4-Dioxygenase Alpha Chain
Chain: A, C, E, G, I, K
Synonym: 3,4-Pcd
Ec: 1.13.11.3
Engineered: Yes
Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Gene: Pcag
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protocatechuate 3,4-Dioxygenase Beta Chain
Chain: B, D, F, H, J, L
Synonym: 3,4-Pcd
Ec: 1.13.11.3
Engineered: Yes
Mutation: Yes

Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Gene: Pcah
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 1 2 1
R_factor 0.149 R_Free 0.192
crystal
cell
length a length b length c angle alpha angle beta angle gamma
195.821 128.569 134.356 90.00 97.98 90.00
method X-Ray Diffractionresolution 2.06 Å
ligand CME, DHB, FE enzyme Oxidoreductase E.C.1.13.11.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, E, C, I, G


F, J, B, H, D, L


Primary referenceRoles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis., Valley MP, Brown CK, Burk DL, Vetting MW, Ohlendorf DH, Lipscomb JD, Biochemistry 2005 Aug 23;44(33):11024-39. PMID:16101286
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (456 Kb) [Save to disk]
  • Biological Unit Coordinates (1ykn.pdb1.gz) 870 Kb
  • LPC: Ligand-Protein Contacts for 1YKN
  • CSU: Contacts of Structural Units for 1YKN
  • Likely Quarternary Molecular Structure file(s) for 1YKN
  • Structure Factors (1288 Kb)
  • Retrieve 1YKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YKN from S2C, [Save to disk]
  • Re-refined 1ykn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YKN 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 1YKN
  • 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 1YKN, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ykn_D] [1ykn_L] [1ykn_A] [1ykn_B] [1ykn_G] [1ykn_H] [1ykn] [1ykn_J] [1ykn_C] [1ykn_E] [1ykn_I] [1ykn_K] [1ykn_F]
  • SWISS-PROT database: [P00436] [P00437]
  • Domain organization of [PCXA_PSEPU] [PCXB_PSEPU] by SWISSPFAM
  • Other resources with information on 1YKN
  • Community annotation for 1YKN 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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