1OOK

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

Structural Biology Knowledgebase: 1OOK SBKB.org


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 1OOK

Classification: HYDROLASE

Total Structure Weight: 67931.20

Macromolecule Entities
Molecule Chains Length Organism Details
Human Alpha Thrombin A 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN A CHAIN
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Human Alpha Thrombin B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN B CHAIN
Gene Name(s): F2 Gene View
PHE-PRO-ARG-Chloromethylketone P 3 synthetic
Platelet glycoprotein Ib alpha chain precursor G 290 Homo sapiens Fragment: N-terminal domain
Mutation: C65A, Y276X, Y279X
Gene Name(s): GP1BA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

B, G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on 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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.65 α = 90.00
b = 67.65 β = 90.00
c = 328.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4