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Cryo-EM structure of vwf D'D3 dimer (wild type) complexed with D1D2 at 3.4 angstron resolution (1 unit)
Analyse Cryo-EM structure of vwf D'D3 dimer (wild type) complexed with D1D2 at 3.4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WN4
- 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 0.80
Structure
electron microscopy · 2 distinct chains · 17% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | Von willebrand antigen 2 | protein | 711 | 17% helix, 24% strand | P04275 |
| F, H | Von willebrand factor | protein | 475 | 16% helix, 17% strand | P04275 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains E, F, G, H
- 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 | 588 | 0.80 | 0.85 | 91 | empty |
| 2 | 901 | 0.77 | 0.80 | 99 | empty |
| 3 | 420 | 0.77 | 0.86 | 60 | empty |
| 4 | 688 | 0.76 | 0.82 | 76 | empty |
| 5 | 569 | 0.75 | 0.82 | 58 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2895 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2800 Ų buried · 29 hydrogen bonds · protein-protein
- E–G · 1846 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 1333 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 141 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 116 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7WN4 · Cryo-EM structure of VWF D'D3 dimer (wild type) complexed with D1D2 at 3.4 angstron… · 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 7WN4 · PDBe 7WN4 · UniProt P04275
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