MolNFT v1 · #84632 · protein
Von willebrand factor A2 domain with calcium
3ZQK: “Von willebrand factor A2 domain with calcium”. X-ray diffraction, 2 ligands (NAG, CA), 2 pockets (best druggability 0.43). MolNFT v1 #84632 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZQK
- Type
- protein
- Length
- 537 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor
- UniProt
- P04275
- Ligands
- NAG, CA
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Von willebrand factor | protein | 181 | 35% helix, 22% strand | P04275 |
| B, C | Von willebrand factor | protein | 178 | 34% helix, 22% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.43 | 0.75 | 35 | empty |
| 2 | 145 | 0.40 | 0.74 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 554 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 416 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 3ZQK · Von Willebrand Factor A2 domain with calcium · the same entry in another collection · chain A against A, 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 3ZQK · PDBe 3ZQK · UniProt P04275
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