MolNFT v1 · #157523 · protein
Crystal structure of monomeric von willebrand factor D`D3 assembly
6N29: “Crystal structure of monomeric von willebrand factor D`D3 assembly”. X-ray diffraction, 2 ligands (NAG, CA), 14 pockets (best druggability 0.65). MolNFT v1 #157523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N29
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand factor
- UniProt
- P04275
- Ligands
- NAG, CA
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Von willebrand factor | protein | 478 | 16% helix, 32% strand | P04275 |
| B | Von willebrand factor | protein | 475 | 16% helix, 32% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.65 | 0.78 | 50 | empty |
| 2 | 228 | 0.61 | 0.81 | 35 | empty |
| 3 | 354 | 0.59 | 0.76 | 44 | empty |
| 4 | 325 | 0.57 | 0.76 | 37 | empty |
| 5 | 276 | 0.56 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 998 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6N29 · Crystal structure of monomeric von Willebrand Factor D`D3 assembly · 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 6N29 · PDBe 6N29 · UniProt P04275
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