1OOK Hydrolase date Mar 03, 2003
title Crystal Structure Of The Complex Of Platelet Receptor Gpib-A Human Alpha-Thrombin
authors K.I.Varughese, R.Celikel, Z.M.Ruggeri
compound source
Molecule: Human Alpha Thrombin
Chain: A
Fragment: Thrombin A Chain
Synonym: Coagulation Factor II
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Purified From Plasma

Molecule: Human Alpha Thrombin
Chain: B
Fragment: Thrombin B Chain
Synonym: Coagulation Factor II

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

Molecule: Phe-Pro-Arg-Chloromethylketone
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized

Molecule: Platelet Glycoprotein Ib Alpha Chain Precursor
Chain: G
Fragment: N-Terminal Domain
Synonym: Glycoprotein Ib-Alpha, Gp-Ib Alpha, Gpiba, Gpib-Al
Cd42b, [Part Of: Glycocalicin]
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gp1ba
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.212 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
67.649 67.649 328.578 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CL, MAN, NAG, TYS enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1HAI, 1M0Z, 1NY2, 1SG8, 1SQ0


Primary referenceModulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha., Celikel R, McClintock RA, Roberts JR, Mendolicchio GL, Ware J, Varughese KI, Ruggeri ZM, Science 2003 Jul 11;301(5630):218-21. PMID:12855810
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (1ook.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 1OOK
  • CSU: Contacts of Structural Units for 1OOK
  • Likely Quarternary Molecular Structure file(s) for 1OOK
  • Structure Factors (369 Kb)
  • Retrieve 1OOK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OOK from S2C, [Save to disk]
  • Re-refined 1ook structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OOK 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 1OOK
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1OOK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ook.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1ookg_, region G [Jmol] [rasmolscript] [script source]
  • Fold representative 1ook 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: [1ook_G] [1ook_P] [1ook_B] [1ook] [1ook_A]
  • SWISS-PROT database: [P07359] [P00734]
  • Domain organization of [GP1BA_HUMAN] [THRB_HUMAN] by SWISSPFAM
  • Domains found in 1OOK: [LRR] [LRRCT] [LRRNT] [LRR_TYP] [Tryp_SPc ] by SMART
  • Other resources with information on 1OOK
  • Community annotation for 1OOK 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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