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Cryo-EM structure of vwf D'D3 dimer complexed with D1D2 at 2.85 angstron resolution (1 unit)
Analyse Cryo-EM structure of vwf D'D3 dimer complexed with D1D2 at 2.85 angstron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPP
- Type
- protein
- Length
- 2,372 residues
- Chains
- 4
- 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 0.83
Structure
electron microscopy · 2 distinct chains · 14% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | Von willebrand antigen 2 | protein | 711 | 15% helix, 27% strand | P04275 |
| F, H | Von willebrand factor | protein | 475 | 13% helix, 22% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains E, F, H, G
- CA · Calcium ion · metal · 6 copies · chains 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 | 829 | 0.83 | 0.85 | 108 | empty |
| 2 | 667 | 0.81 | 0.86 | 93 | empty |
| 3 | 435 | 0.77 | 0.86 | 62 | empty |
| 4 | 644 | 0.76 | 0.82 | 84 | empty |
| 5 | 331 | 0.76 | 0.87 | 46 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2719 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2664 Ų buried · 35 hydrogen bonds · protein-protein
- E–G · 1885 Ų buried · 25 hydrogen bonds · protein-protein
- F–H · 1377 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 116 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7WPP · Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 2.85 angstron resolution (1… · the same entry in another collection · chain E against E, 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 7WPP · PDBe 7WPP · UniProt P04275
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