Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.25 kDa 
• Atom Count: 2426 
• Residue Count: 280 
• Unique protein chains: 2

3P72

structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor

• DOI: 10.2210/pdb3P72/pdb

• Classification: Blood Clotting/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-10-12 Released: 2010-11-24 
• Deposition Author(s): McEwan, P.A., Andrews, R.K., Emsley, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.217 
• R-Value Observed: 0.221 

Literature

Glycoprotein Ibalpha inhibitor complex structure reveals a combined steric and allosteric mechanism of von Willebrand factor antagonism.

McEwan, P.A., Andrews, R.K., Emsley, J.

(2009) Blood 114: 4883-4885

• PubMed: 19726719 
• DOI: 10.1182/blood-2009-05-224170
• Primary Citation of Related Structures:  
  3P72


• PubMed Abstract: 
  

Platelet glycoprotein Ibalpha (GpIbalpha) interactions with von Willebrand factor (VWF) are a critical early event in platelet adhesion, which contributes to hemostasis and thrombosis. Here we report the structure of a complex between GpIbalpha and a potent peptide inhibitor. The cyclic peptide (CTERMALHNLC) was isolated from a cysteine-constrained phage display library, and in the complex this forms one and a half turns of an amphipathic alpha-helix, the curvature of which facilitates contacts with the curved concave face of the GpIbalpha leucine-rich repeats. The peptide has only limited overlap with the VWF binding site. It effectively inhibits by stabilizing an alternative alpha-helical conformation of a regulatory loop that forms an extended beta-hairpin upon VWF binding. The structure defines a previously unrecognized binding site within GpIbalpha and represents a clear strategy for developing antiplatelet agents targeting the GpIbalpha-VWF interaction allosterically.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib alpha chain	A	269	Homo sapiens	Mutation(s): 2  Gene Names: GP1BA
Find proteins for P07359 (Homo sapiens) Explore P07359  Go to UniProtKB:  P07359
NIH Common Fund Data Resources
PHAROS:  P07359 GTEx:  ENSG00000185245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OS1 peptide	B	11	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000829	B	OS1 peptide	Oligopeptide /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.217 
• R-Value Observed: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.817	α = 90
b = 58.817	β = 90
c = 163.027	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-12 
• Released Date: 2010-11-24 
Deposition Author(s): McEwan, P.A., Andrews, R.K., Emsley, J.

Revision History 

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2018-10-10
  Changes: Data collection, Database references, Structure summary