5OU9

Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet glycoprotein VIA, B181Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
(GPO)3C, D, E21Homo sapiensMutation(s): 0 
Gene Names: COL1A1
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens)
Explore P02452 
Go to UniProtKB:  P02452
PHAROS:  P02452
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A], I [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A], J [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
C, D, EL-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.72α = 90
b = 59.72β = 90
c = 319.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organization for Scientific ResearchNetherlandsECHO 700.58.006

Revision History  (Full details and data files)

  • 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