Download MendeleyStructural 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.
5OU9
Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
- PDB DOI: 10.2210/pdb5OU9/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2017-08-23 Released: 2018-09-05
- Funding Organization(s): Netherlands Organization for Scientific Research
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
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Platelet glycoprotein VI | A, B | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HCN6 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| (GPO)3 | C, D, E | 21 | Homo sapiens | Mutation(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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02452 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | 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 | G [auth A], J [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | H [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| HYP Query on HYP | C, D, E | L-PEPTIDE LINKING | C5 H9 N O3 |  | PRO |
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 = 59.72 | α = 90 |
| b = 59.72 | β = 90 |
| c = 319.72 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-09-05 Deposition Author(s): Feitsma, L.J., Huizinga, E.G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Netherlands Organization for Scientific Research | Netherlands | ECHO 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
