4GD3 Structure of E. coli hydrogenase-1 in complex with cytochrome b date 2012-07-31
authors Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.
compound source
symmetry
R_factor
R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.30
ligand CL, F4S, FCO, HEM, LMT, MG, NI, SF4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


J, K, M, L
  • electron transfer activity


    • S, T, Q, R
  • electron transfer activity


    • Primary referenceCrystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b., Volbeda A, Darnault C, Parkin A, Sargent F, Armstrong FA, Fontecilla-Camps JC, Structure. 2012 Dec 19. pii: S0969-2126(12)00425-X. doi:, 10.1016/j.str.2012.11.010. PMID:23260654
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1325 Kb) [Save to disk]
  • Biological Unit Coordinates (4gd3.pdb1.gz) 660 Kb
  • Biological Unit Coordinates (4gd3.pdb2.gz) 304 Kb
  • Biological Unit Coordinates (4gd3.pdb3.gz) 366 Kb
  • Biological Unit Coordinates (4gd3.pdb4.gz) 660 Kb
  • Biological Unit Coordinates (4gd3.pdb5.gz) 304 Kb
  • Biological Unit Coordinates (4gd3.pdb6.gz) 366 Kb
  • LPC: Ligand-Protein Contacts for 4GD3
  • CSU: Contacts of Structural Units for 4GD3
  • Structure Factors (948 Kb)
  • Retrieve 4GD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GD3 from S2C, [Save to disk]
  • Re-refined 4gd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4GD3 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 4GD3
  • 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 4GD3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gd3_R] [4gd3_L] [4gd3_S] [4gd3_B] [4gd3_K] [4gd3_T] [4gd3_M] [4gd3] [4gd3_Q] [4gd3_J] [4gd3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4GD3
  • Community annotation for 4GD3 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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