Research workbench
Vwf tubules of D1D2D'D3 domains
Analyse Vwf tubules of D1D2D'D3 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PNF
- Type
- protein
- Length
- 2,282 residues
- Chains
- 2
- 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 0.84
Structure
electron microscopy · 1 distinct chain · 13% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Von willebrand factor | protein | 1141 | 13% helix, 20% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 6 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.84 | 0.85 | 124 | empty |
| 2 | 1148 | 0.83 | 0.84 | 106 | empty |
| 3 | 682 | 0.78 | 0.83 | 72 | empty |
| 4 | 836 | 0.78 | 0.81 | 75 | empty |
| 5 | 738 | 0.75 | 0.81 | 86 | empty |
Interfaces
1 interface between chains.
- B–D · 1466 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 108 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7PNF · VWF Tubules of D1D2D'D3 domains · the same entry in another collection · chain B against B, 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 7PNF · PDBe 7PNF · UniProt P04275
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