Research workbench
Structure of a novel antithrombotic agent agkisacucetin in complex with the platelet glycoprotein ib receptor
Analyse Structure of a novel antithrombotic agent agkisacucetin in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XFQ
- Type
- protein
- Length
- 527 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein ib alpha chain; Snaclec agglucetin subunit alpha-1; Snaclec…
- UniProt
- P07359, Q8JIV9, Q8AYA3
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Platelet glycoprotein ib alpha chain | protein | 273 | 10% helix, 13% strand | P07359 |
| A | Snaclec agglucetin subunit alpha-1 | protein | 130 | 17% helix, 31% strand | Q8JIV9 |
| B | Snaclec agglucetin subunit beta-2 | protein | 124 | 20% helix, 35% strand | Q8AYA3 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.84 | 0.95 | 56 | empty |
| 2 | 613 | 0.67 | 0.77 | 43 | empty |
| 3 | 59 | 0.67 | 0.94 | 18 | empty |
| 4 | 74 | 0.49 | 0.83 | 18 | empty |
| 5 | 187 | 0.48 | 0.76 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1879 Ų buried · 26 hydrogen bonds · protein-protein
- G–B · 781 Ų buried · 11 hydrogen bonds · protein-protein
- G–A · 393 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6XFQ · Structure of a novel antithrombotic agent Agkisacucetin in complex with the platelet… · the same entry in another collection · chain G against G, TM-score 1.00
- Q8AYA3 · AlphaFold monomer V2.0 prediction for snaclec agglucetin subunit beta-2 (Q8AYA3) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q8JIV9 · AlphaFold monomer V2.0 prediction for snaclec agglucetin subunit alpha-1 (Q8JIV9) · a predicted model of the same protein · chain A against A, TM-score 0.97
- 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 P07359
- Every structure of UniProt Q8JIV9
- Every structure of UniProt Q8AYA3
- Elsewhere: RCSB PDB 6XFQ · PDBe 6XFQ · UniProt P07359 · UniProt Q8JIV9 · UniProt Q8AYA3
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