1P8V Membrane Protein Hydrolase date May 07, 2003
title Crystal Structure Of The Complex Of Platelet Receptor Gpib-A Alpha-Thrombin At 2.6a
authors J.J.Dumas, R.Kumar, J.Seehra, W.S.Somers, L.Mosyak
compound source
Molecule: Platelet Glycoprotein Ib Alpha Chain
Chain: A
Fragment: Glycoprotein 1b Alpha
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gp1ba
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_organ: Ovary Cells

Molecule: Prothrombin
Chain: B
Fragment: Alpha Thrombin, Light Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Isolated From Human Plasma

Molecule: Prothrombin
Chain: C
Fragment: Alpha Thrombin, Heavy Chain
Synonym: Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Isolated From Human Plasma
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.095 111.770 176.251 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand DFP, MES, NAG, TYS enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1C4Y, 1HDT, 1QYY, 1SQ0
Gene
Ontology
ChainFunctionProcessComponent
B


C


Primary referenceCrystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation., Dumas JJ, Kumar R, Seehra J, Somers WS, Mosyak L, Science 2003 Jul 11;301(5630):222-6. PMID:12855811
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (1p8v.pdb1.gz) 185 Kb
  • LPC: Ligand-Protein Contacts for 1P8V
  • CSU: Contacts of Structural Units for 1P8V
  • Likely Quarternary Molecular Structure file(s) for 1P8V
  • Retrieve 1P8V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1P8V from S2C, [Save to disk]
  • View 1P8V 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 1P8V
  • 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 1P8V, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p8va_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1p8v.1, region B:,C [Jmol] [rasmolscript] [script source]
  • Fold representative 1p8v 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: [1p8v_C] [1p8v] [1p8v_A] [1p8v_B]
  • SWISS-PROT database: [P07359] [P00734]
  • Domain organization of [GP1BA_HUMAN] [THRB_HUMAN] by SWISSPFAM
  • Domains found in 1P8V: [LRR] [LRRCT] [LRRNT] [LRR_TYP] [Tryp_SPc ] by SMART
  • Other resources with information on 1P8V
  • Community annotation for 1P8V 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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