3PMH Blood Cloting, Hydrolase Inhibitor date Nov 16, 2010
title Mechanism Of Sulfotyrosine-Mediated Glycoprotein Ib Interact Two Distinct Alpha-Thrombin Sites
authors K.I.Varughese, R.Celikel
compound source
Molecule: Thrombin Alpha-Chain
Chain: A
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: From Human Plasma

Molecule: Thrombin Beta-Chain
Chain: B
Synonym: Coagulation Factor II
Ec: 3.4.21.5

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

Molecule: Platelet Glycoprotein Ib Alpha Chain
Chain: G
Fragment: Unp Residues 17-306
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gp1ba, Platelet Glycoprotein Ib Alpha
Expression_system: Drosophila Melanogaster
Expression_system_taxid: 7227
symmetry Space Group: P 43 21 2
R_factor 0.220 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.657 67.657 329.730 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand 0G7, MAN, NAG, TYS enzyme Hydrolase E.C.3.4.21.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceBinding of {alpha}-thrombin to surface-anchored platelet glycoprotein Ib{alpha} sulfotyrosines through a two-site mechanism involving exosite I., Zarpellon A, Celikel R, Roberts JR, McClintock RA, Mendolicchio GL, Moore KL, Jing H, Varughese KI, Ruggeri ZM, Proc Natl Acad Sci U S A. 2011 May 24;108(21):8628-33. Epub 2011 May 9. PMID:21555542
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (3pmh.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 3PMH
  • CSU: Contacts of Structural Units for 3PMH
  • Structure Factors (175 Kb)
  • Retrieve 3PMH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PMH from S2C, [Save to disk]
  • Re-refined 3pmh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PMH 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 3PMH
  • 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 3PMH, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pmh_G] [3pmh_B] [3pmh] [3pmh_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PMH: [LRR] [LRRCT] [LRRNT] [LRR_TYP] [Tryp_SPc ] by SMART
  • Other resources with information on 3PMH
  • Community annotation for 3PMH 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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