Research workbench
Cryo-EM structure of vwf D'D3 dimer complexed with D1D2 at 3.27 angstron resolution (2 units)
Analyse Cryo-EM structure of vwf D'D3 dimer complexed with D1D2 at 3.27 angstron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPQ
- 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, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | Von willebrand antigen 2 | protein | 711 | 15% helix, 26% strand | P04275 |
| C, D, F, H | Von willebrand factor | protein | 478 | 12% helix, 20% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
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 | 950 | 0.84 | 0.85 | 117 | empty |
| 2 | 1174 | 0.82 | 0.84 | 132 | empty |
| 3 | 960 | 0.81 | 0.83 | 101 | empty |
| 4 | 873 | 0.81 | 0.83 | 96 | empty |
| 5 | 738 | 0.81 | 0.85 | 91 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2678 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2661 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2646 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2626 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 1937 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 232 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 7WPQ · Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 3.27 angstron resolution (2… · 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 7WPQ · PDBe 7WPQ · UniProt P04275
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