MolNFT v1 · #191116 · protein
Vwf tubules of D1D2 and D'D3A1 domains
7ZWH · Von willebrand factor: “Vwf tubules of D1D2 and D'D3A1 domains”. Electron microscopy, 3 ligands (NAG, BMA, CA), 20 pockets (best druggability 0.85). MolNFT v1 #191116 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZWH
- Type
- protein
- Length
- 2,660 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor
- UniProt
- P04275
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 19% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | Von willebrand factor | protein | 1131 | 16% helix, 18% strand | P04275 |
| G, H | Von willebrand factor | protein | 199 | 35% helix, 17% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains D, E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 6 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.85 | 0.86 | 106 | empty |
| 2 | 951 | 0.85 | 0.86 | 127 | empty |
| 3 | 669 | 0.80 | 0.84 | 86 | empty |
| 4 | 715 | 0.77 | 0.82 | 70 | empty |
| 5 | 510 | 0.74 | 0.83 | 78 | empty |
Interfaces
3 interfaces between chains.
- D–E · 3432 Ų buried · 38 hydrogen bonds · protein-protein
- E–G · 731 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 279 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 110 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZWH · VWF Tubules of D1D2 and D'D3A1 domains · the same entry in another collection · chain D against D, TM-score 1.00
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
- Elsewhere: RCSB PDB 7ZWH · PDBe 7ZWH · UniProt P04275
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