1D2O Structural Protein date Sep 25, 1999
title Crystal Structure Of A Single B Repeat Unit (B1) Of Collagen Binding Surface Protein (Cna) Of Staphylococcus Aureus.
authors C.C.S.Deivanayagam, R.L.Rich, M.Hook, S.V.L.Narayana
compound source
Molecule: Collagen Adhesin
Chain: A, B
Fragment: Single B Repeat Unit
Synonym: Cna
Engineered: Yes
Organism_scientific: Staphylococcus Aureus
Organism_common: Bacteria
Expression_system: Escherichia Coli
Expression_system_common: Bacteria
Expression_system_plasmid: Pq3-30
Other_details: Bacteria
symmetry Space Group: I 2 2 2
R_factor 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.907 101.538 121.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
note 1D2O is a representative structure
related structures by homologous chain: 1D2P
similarity Belongs to the Collagen_bind family.
subcellular loc. Attached to the cell wall peptidoglycan by an amide bond (potential).
Gene CNA (S. aureus)
function Mediates attachment of staphyococcal cells to collagen- containing substrata.
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • binding
  • collagen binding

  • cell wall
  • cell surface
  • Primary referenceNovel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein., Deivanayagam CC, Rich RL, Carson M, Owens RT, Danthuluri S, Bice T, Hook M, Narayana SV, Structure Fold Des 2000 Jan 15;8(1):67-78. PMID:10673425
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (1d2o.pdb1.gz) 63 Kb
  • CSU: Contacts of Structural Units for 1D2O
  • Likely Quarternary Molecular Structure file(s) for 1D2O
  • Retrieve 1D2O in mmCIF format [Save to disk]
  • View 1D2O 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
  • Visual 3D analysis of 1D2O
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D2O, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d2oa1, region A:535-624 [Jmol] [rasmolscript] [script source]
        - Domain d1d2oa2, region A:625-721 [Jmol] [rasmolscript] [script source]
        - Domain d1d2ob1, region B:535-624 [Jmol] [rasmolscript] [script source]
        - Domain d1d2ob2, region B:625-721 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d2o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d2o_A] [1d2o_B]
  • Other resources with information on 1D2O
  • InterPro: IPR001899 , IPR008456 , IPR008454
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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