Research workbench
Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 4.3 angstron resolution (7 units)
Analyse Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 4.3 angstron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPS
- Type
- protein
- Length
- 16,646 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.32
- Source
- Homo sapiens
- Molecule
- von Willebrand antigen 2; von Willebrand factor
- UniProt
- P04275
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 4.32 · 2 distinct chains · 14% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, I, K, M, O, Q, S, U, W, Y, a | von Willebrand antigen 2 | protein | 711 | 15% helix, 25% strand | P04275 |
| Z, b, C, D, F, H, J, L, N, P, R, T, V, X | von Willebrand factor | protein | 478 | 12% helix, 19% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, Z, B, E, G, I, K, Q, S, U, W, a, C, D, F, H, J, L, R, T, V, X
- CA · Calcium ion · metal · 56 copies · chains A, Z, B, b, E, G, I, K, M, O, Q, S, U, W, Y, a, C, D, F, H, J, L, N, P, R, T, V, X
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 | 1021 | 0.85 | 0.86 | 122 | empty |
| 2 | 1004 | 0.84 | 0.85 | 126 | empty |
| 3 | 956 | 0.84 | 0.86 | 111 | empty |
| 4 | 994 | 0.84 | 0.85 | 119 | empty |
| 5 | 1007 | 0.84 | 0.85 | 129 | empty |
Interfaces
63 interfaces between chains.
- Z–Y · 2676 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 2674 Ų buried · 32 hydrogen bonds · protein-protein
- U–V · 2672 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2669 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2668 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 812 disulfide, 42 glycan (disulfide, N-glycosylation).
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 7WPS · PDBe 7WPS · UniProt P04275
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