2VDF Membrane Protein date Oct 05, 2007
title Structure Of The Opca Adhesion From Neisseria Meningitidis D By Crystallization From The Cubic Mesophase
authors V.Cherezov, W.Liu, J.P.Derrick, B.Luan, A.Aksimentiev, V.Katritch M.Caffrey
compound source
Molecule: Outer Membrane Protein
Chain: A
Synonym: Opca
Engineered: Yes
 Organism_scientific: Neisseria Meningitidis
Organism_taxid: 487
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.860 42.500 150.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand OCT, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • aspartic-type endopeptidase ...


    • Primary referenceIn meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin., Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, Katritch V, Caffrey M, Proteins. 2007 Dec 12;. PMID:18076035
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2vdf.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2VDF
  • CSU: Contacts of Structural Units for 2VDF
  • Likely Quarternary Molecular Structure file(s) for 2VDF
  • Structure Factors (134 Kb)
  • Retrieve 2VDF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VDF from S2C, [Save to disk]
  • Re-refined 2vdf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VDF 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 2VDF
  • 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 2VDF, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vdf_A] [2vdf]
  • SWISS-PROT database: [Q9AE79]
  • Domain organization of [Q9AE79_NEIME] by SWISSPFAM
    • Other resources with information on 2VDF
  • Community annotation for 2VDF 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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