MolNFT v1 · #190212 · protein
Cryo-EM structure of vwf D'D3 dimer (R1136M/E1143M mutant) complexed with D1D2 at 3.29 angstron resolution (2 units)
7WN6 · Von willebrand antigen 2: “Cryo-EM structure of vwf D'D3 dimer (R1136M/E1143M mutant) complexed with D1D2 at 3.29 angstron resolution (2…”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 7WN6
- Type
- protein
- Length
- 4,756 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Von willebrand antigen 2; Von willebrand factor
- UniProt
- P04275
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 14% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | Von willebrand antigen 2 | protein | 711 | 16% helix, 25% strand | P04275 |
| F, H, C, D | Von willebrand factor | protein | 478 | 12% helix, 18% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, F, H, B, E, G, C, D
- CA · Calcium ion · metal · 16 copies · chains A, F, B, H, E, G, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.84 | 0.86 | 107 | empty |
| 2 | 766 | 0.83 | 0.86 | 110 | empty |
| 3 | 1186 | 0.83 | 0.84 | 133 | empty |
| 4 | 980 | 0.82 | 0.84 | 97 | empty |
| 5 | 671 | 0.82 | 0.86 | 85 | empty |
Interfaces
15 interfaces between chains.
- A–C · 3028 Ų buried · 41 hydrogen bonds · protein-protein
- H–G · 2884 Ų buried · 34 hydrogen bonds · protein-protein
- F–E · 2602 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 2262 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 230 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 7WN6 · Cryo-EM structure of VWF D'D3 dimer (R1136M/E1143M mutant) complexed with D1D2 at 3.29… · 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 7WN6 · PDBe 7WN6 · UniProt P04275
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