2D0V Oxidoreductase date Aug 09, 2005
title Crystal Structure Of Methanol Dehydrogenase From Hyphomicrobium Denitrificans
authors M.Nojiri, D.Hira, K.Yamaguchi, S.Suzuki
compound source
Molecule: Methanol Dehydrogenase Large Subunit
Chain: A, D, I
Ec: 1.1.99.8
Organism_scientific: Hyphomicrobium Denitrificans
Organism_taxid: 53399
Strain: A3151

Molecule: Methanol Dehydrogenase Small Subunit
Chain: B, E, J
Ec: 1.1.99.8

Organism_scientific: Hyphomicrobium Denitrificans
Organism_taxid: 53399
Strain: A3151
symmetry Space Group: C 1 2 1
R_factor 0.149 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
291.320 63.999 109.941 90.00 105.74 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand CA, PQQ enzyme Oxidoreductase E.C.1.1.99.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, I


J, E, B


Primary referenceCrystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins., Nojiri M, Hira D, Yamaguchi K, Okajima T, Tanizawa K, Suzuki S, Biochemistry. 2006 Mar 21;45(11):3481-92. PMID:16533029
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (337 Kb) [Save to disk]
  • Biological Unit Coordinates (2d0v.pdb1.gz) 225 Kb
  • Biological Unit Coordinates (2d0v.pdb2.gz) 221 Kb
  • LPC: Ligand-Protein Contacts for 2D0V
  • CSU: Contacts of Structural Units for 2D0V
  • Likely Quarternary Molecular Structure file(s) for 2D0V
  • Structure Factors (522 Kb)
  • Retrieve 2D0V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D0V from S2C, [Save to disk]
  • Re-refined 2d0v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D0V 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 2D0V
  • 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 2D0V, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d0v] [2d0v_B] [2d0v_J] [2d0v_D] [2d0v_I] [2d0v_E] [2d0v_A]
  • SWISS-PROT database: [Q4AE23] [Q4AE26]
  • Domain organization of [Q4AE23_9RHIZ] [Q4AE26_9RHIZ] by SWISSPFAM
  • Domain found in 2D0V: [PQQ ] by SMART
  • Other resources with information on 2D0V
  • Community annotation for 2D0V 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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