1QYY

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

• PDB DOI: https://doi.org/10.2210/pdb1QYY/pdb

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


• 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: 2.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.17 kDa 
• Atom Count: 4,277 
• Modelled Residue Count: 532 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib alpha chain	A, B [auth G]	290	Homo sapiens	Mutation(s): 1  Gene Names: GP1BA
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens) Explore P07359  Go to UniProtKB:  P07359
PHAROS:  P07359 GTEx:  ENSG00000185245

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PT	D [auth A], E [auth A], G	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.282 
• R-Value Work: 0.219 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.61	α = 90
b = 113.82	β = 95.21
c = 56.21	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-27
  Changes: Database references, Structure summary
• Version 2.2: 2024-04-03
  Changes: Data collection, Refinement description