1H8P Phosphorylcholine-Binding Protein date Feb 14, 2001
title Bull Seminal Plasma Pdc-109 Fibronectin Type II Module
authors D.A.Wah, C.Fernandez-Tornero, J.J.Calvete, A.Romero
compound source
Molecule: Seminal Plasma Protein Pdc-109
Chain: A, B
Fragment: Residues 26-134
 Organism_scientific: Bos Taurus
Organism_common: Bull
Organism_taxid: 9913
Tissue: Sperm
symmetry Space Group: P 3 2 1
R_factor 0.207 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.881 90.881 52.210 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.82 Å
ligand PC enzyme
note 1H8P is a representative structure
related structures by homologous chain: 1PDC
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSperm coating mechanism from the 1.8 A crystal structure of PDC-109-phosphorylcholine complex., Wah DA, Fernandez-Tornero C, Sanz L, Romero A, Calvete JJ, Structure (Camb) 2002 Apr;10(4):505-14. PMID:11937055
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1h8p.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 1H8P
  • CSU: Contacts of Structural Units for 1H8P
  • Likely Quarternary Molecular Structure file(s) for 1H8P
  • Structure Factors (158 Kb)
  • Retrieve 1H8P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1H8P from S2C, [Save to disk]
  • Re-refined 1h8p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1H8P 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 1H8P
  • 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 1H8P, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h8pa1, region A:22-67 [Jmol] [rasmolscript] [script source]
        - Domain d1h8pa2, region A:68-109 [Jmol] [rasmolscript] [script source]
        - Domain d1h8pb1, region B:22-67 [Jmol] [rasmolscript] [script source]
        - Domain d1h8pb2, region B:68-109 [Jmol] [rasmolscript] [script source]
  • 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: [1h8p_A] [1h8p] [1h8p_B]
  • SWISS-PROT database: [P02784]
  • Domain organization of [SFP1_BOVIN] by SWISSPFAM
  • Domain found in 1H8P: [FN2 ] by SMART
    • Other resources with information on 1H8P
  • Community annotation for 1H8P 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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