MolNFT v1 · #17289 · protein
Crystal structure of the complex of platelet receptor gpib-alpha and human alpha-thrombin
1OOK · Human alpha thrombin: “Crystal structure of the complex of platelet receptor gpib-alpha and human alpha-thrombin”. X-ray diffraction, 3 ligands (NAG, MAN, CL), 6 pockets (best druggability 0.73). MolNFT v1 #17289 on GenesisL1: 3D…
- PDB
- 1OOK
- Type
- protein
- Length
- 582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human alpha thrombin; Phe-pro-arg-chloromethylketone; Platelet glycoprotein ib alpha…
- EC
- 3.4.21.5
- UniProt
- P00734, P07359
- Ligands
- NAG, MAN, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human alpha thrombin (EC 3.4.21.5) | protein | 36 | 25% helix, 0% strand | P00734 |
| B | Human alpha thrombin (EC 3.4.21.5) | protein | 259 | 12% helix, 34% strand | P00734 |
| P | Phe-pro-arg-chloromethylketone | protein | 3 | 0% helix, 33% strand | — |
| G | Platelet glycoprotein ib alpha chain precursor | protein | 284 | 8% helix, 17% strand | P07359 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, G
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- CL · Chloride ion · ion · chains B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.73 | 0.78 | 60 | CL |
| 2 | 111 | 0.49 | 0.81 | 26 | empty |
| 3 | 163 | 0.49 | 0.78 | 23 | empty |
| 4 | 137 | 0.48 | 0.78 | 18 | empty |
| 5 | 148 | 0.45 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1322 Ų buried · 27 hydrogen bonds · protein-protein
- B–G · 1185 Ų buried · 25 hydrogen bonds · protein-protein
- B–P · 450 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 1OOK · Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin · 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 G against A, TM-score 0.94
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 P00734
- Every structure of UniProt P07359
- Elsewhere: RCSB PDB 1OOK · PDBe 1OOK · UniProt P00734 · UniProt P07359
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.