3X26 Lyase date Dec 10, 2014
title Crystal Structure Of Nitrile Hydratase Mutant Br56k Complexe Trimethylacetonitrile, Photo-Activated For 5 Min
authors Y.Yamanaka, K.Hashimoto, K.Noguchi, M.Yohda, M.Odaka
compound source
Molecule: Nitrile Hydratase Subunit Alpha
Chain: A
Synonym: Nhase, Nitrilase
Ec: 4.2.1.84
Engineered: Yes
Organism_scientific: Rhodococcus Erythropolis
Organism_taxid: 1833
Gene: Ntha
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nitrile Hydratase Subunit Beta
Chain: B
Synonym: Nhase, Nitrilase
Ec: 4.2.1.84
Engineered: Yes
Mutation: Yes

Organism_scientific: Rhodococcus Erythropolis
Organism_taxid: 1833
Gene: Nthb, Nha2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.173 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.861 59.953 81.594 90.00 125.08 90.00
method X-Ray Diffractionresolution 1.34 Å
ligand CL, CSD, CSO, FE, MG, TAN enzyme Lyase E.C.4.2.1.84 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceTime-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile., Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M, Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10763-7. doi: 10.1002/anie.201502731. PMID:26333053
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3x26.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3X26
  • CSU: Contacts of Structural Units for 3X26
  • Structure Factors (1843 Kb)
  • Retrieve 3X26 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X26 from S2C, [Save to disk]
  • Re-refined 3x26 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X26 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 3X26
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x26] [3x26_A] [3x26_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3X26
  • Community annotation for 3X26 at PDBWiki (http://pdbwiki.org)

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