5OU7 | pdb_00005ou7

Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN

• PDB DOI: https://doi.org/10.2210/pdb5OU7/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-08-23 Released: 2018-09-05 
• Deposition Author(s): Feitsma, L.J., Huizinga, E.G.
• Funding Organization(s): Netherlands Organization for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.260 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.221 (Depositor) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structural insights into collagen-binding by platelet receptor Glycoprotein VI

Feitsma, L.J., Brondijk, T.H.C., Jarvis, G., Hagemans, D., Bihan, D., Jerah, N., Versteeg, M., Farndale, R.W., Huizinga, E.G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.98 kDa 
• Atom Count: 6,101 
• Modeled Residue Count: 702 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein VI	A, B, C, D	181	Homo sapiens	Mutation(s): 0  Gene Names: GP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCN6 (Homo sapiens) Explore Q9HCN6  Go to UniProtKB:  Q9HCN6
PHAROS:  Q9HCN6 GTEx:  ENSG00000088053
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9HCN6-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	K [auth A], S [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
NAG	L [auth A], T [auth B], W [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	J [auth A], R [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], X [auth D], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.260 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.221 (Depositor) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.65	α = 90
b = 44.05	β = 104.69
c = 117.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Feitsma, L.J., Huizinga, E.G.

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Funding Organization	Location	Grant Number
Netherlands Organization for Scientific Research	Netherlands	ECHO 700.58.006

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary