MolNFT v1 · #19925 · protein
Crystal structure of N-terminal domain of human platelet receptor glycoprotein ib-alpha at 2.8 ångström resolution
1QYY · Platelet glycoprotein ib alpha chain: “Crystal structure of N-terminal domain of human platelet receptor glycoprotein ib-alpha at 2.8 ångström…”. X-ray diffraction, 3 ligands (NAG, MAN, PT), 5 pockets (best druggability 0.71).…
- PDB
- 1QYY
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein ib alpha chain
- UniProt
- P07359
- Ligands
- NAG, MAN, PT
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Platelet glycoprotein ib alpha chain | protein | 266 | 11% helix, 15% strand | P07359 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, G
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- PT · Platinum (II) ion · metal · 3 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.71 | 0.85 | 40 | PT |
| 2 | 177 | 0.65 | 0.85 | 25 | empty |
| 3 | 151 | 0.45 | 0.76 | 22 | empty |
| 4 | 152 | 0.44 | 0.75 | 30 | empty |
| 5 | 83 | 0.42 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–G · 812 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1QYY · Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha… · the same entry in another collection · chain A against A, TM-score 1.00
- P07359 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib alpha chain (P07359) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07359
- Elsewhere: RCSB PDB 1QYY · PDBe 1QYY · UniProt P07359
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