Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68002.72 
• Atom Count: 4719 
• Residue Count: 588 
• Unique protein chains: 4

1OOK

Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin

• DOI: 10.2210/pdb1OOK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2003-03-03 Released: 2003-07-22 
• Deposition Author(s): Varughese, K.I., Celikel, R., Ruggeri, Z.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 

Literature

Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha

Celikel, R., McClintock, R.A., Roberts, J.R., Mendolicchio, G.L., Ware, J., Varughese, K.I., Ruggeri, Z.M.

(2003) Science 301: 218-221

• PubMed: 12855810 
• DOI: 10.1126/science.1084183
• Primary Citation of Related Structures:  
  1P9A


• PubMed Abstract: 
  

Thrombin bound to platelets contributes to stop bleeding and, in pathological conditions, may cause vascular thrombosis. We have determined the structure of platelet glycoprotein Ibalpha (GpIbalpha) bound to thrombin at 2.3 angstrom resolution and defined two sites in GpIbalpha that bind to exosite II and exosite I of two distinct alpha-thrombin molecules, respectively. GpIbalpha occupancy may be sequential, as the site binding to alpha-thrombin exosite I appears to be cryptic in the unoccupied receptor but exposed when a first thrombin molecule is bound through exosite II. These interactions may modulate alpha-thrombin function by mediating GpIbalpha clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I.

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Organizational Affiliation: 

Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Thrombosis and Hemostasis, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Human Alpha Thrombin	A	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Human Alpha Thrombin	B	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PHE-PRO-ARG-Chloromethylketone	P	3	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Platelet glycoprotein Ib alpha chain precursor	G	290	Homo sapiens	Mutation(s): 1  Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens) Go to Gene View: GP1BA Go to UniProtKB:  P07359

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAN	B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
NAG	B, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	G	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 67.649	α = 90.00
b = 67.649	β = 90.00
c = 328.578	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
CNS	phasing
SCALEPACK	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-03 
• Released Date: 2003-07-22 
• Deposition Author(s): Varughese, K.I., Celikel, R., Ruggeri, Z.M.

Revision History 

• Version 1.0: 2003-07-22
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance