Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66222.74 
• Atom Count: 4221 
• Residue Count: 580 
• Unique protein chains: 1

1QYY

Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 2.8 Angstrom Resolution

• DOI: 10.2210/pdb1QYY/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): 1 


• Deposited: 2003-09-12 Released: 2004-03-02 
• Deposition Author(s): Varughese, K.I., Ruggeri, Z.M., Celikel, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 

Literature

Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain.

Varughese, K.I., Ruggeri, Z.M., Celikel, R.

(2004) Acta Crystallogr.,Sect.D 60: 405-411

• PubMed: 14993663 
• DOI: 10.1107/S0907444903026805


• PubMed Abstract: 
  

The interaction between platelet glycoprotein (GP) Ib alpha and von Willebrand factor (VWF) is essential for thrombus formation, leading to the arrest of bleeding. The N-terminal domain of GP Ib alpha, which contains the binding sites for VWF and alpha-thrombin, crystallized in the tetragonal space group P4(3) with one molecule in the asymmetric unit. When the crystals were treated with platinum, the crystals changed their symmetry from tetragonal to monoclinic P2(1) with two molecules in the asymmetric unit. The structure of the monoclinic form was solved using two-wavelength platinum anomalous dispersion data. The tetragonal crystal structure was subsequently solved using molecular-replacement techniques using the monoclinic structure as the search model and was refined with 1.7 A resolution data.

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Organizational Affiliation: 

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Platelet glycoprotein Ib alpha chain	A, 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
PT	A, G	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
NAG	A, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 51.610	α = 90.00
b = 113.820	β = 95.21
c = 56.210	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-12 
• Released Date: 2004-03-02 
• Deposition Author(s): Varughese, K.I., Ruggeri, Z.M., Celikel, R.

Revision History 

• Version 1.0: 2004-03-02
  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