Research workbench
The ternary von willebrand factor A1-glycoprotein ibalpha-botrocetin complex
Analyse The ternary von willebrand factor A1-glycoprotein ibalpha-botrocetin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U0N
- Type
- protein
- Length
- 730 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor; Botrocetin; Platelet glycoprotein ib
- UniProt
- P04275, P22029, P22030, P07359
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Von willebrand factor | protein | 207 | 36% helix, 21% strand | P04275 |
| B | Botrocetin | protein | 133 | 20% helix, 30% strand | P22029 |
| C | Botrocetin | protein | 125 | 19% helix, 29% strand | P22030 |
| D | Platelet glycoprotein ib | protein | 265 | 7% helix, 20% strand | P07359 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.79 | 0.80 | 103 | empty |
| 2 | 1192 | 0.78 | 0.80 | 79 | empty |
| 3 | 189 | 0.55 | 0.80 | 34 | empty |
| 4 | 79 | 0.32 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1792 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1080 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 544 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 380 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 1U0N · The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex · the same entry in another collection · chain A against A, TM-score 1.00
- P22029 · AlphaFold monomer V2.0 prediction for snaclec botrocetin subunit alpha (P22029) · a predicted model of the same protein · chain B 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 D against A, TM-score 0.97
- P22030 · AlphaFold monomer V2.0 prediction for snaclec botrocetin subunit beta (P22030) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P04275
- Every structure of UniProt P22029
- Every structure of UniProt P22030
- Every structure of UniProt P07359
- Elsewhere: RCSB PDB 1U0N · PDBe 1U0N · UniProt P04275 · UniProt P22029 · UniProt P22030 · UniProt P07359
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