MolNFT v1 · #137864 · protein
Crystal structure of the human astrovirus 2 oxford serotype capsid protein spike at 1.35-a resolution
5W1N · Capsid polyprotein VP90: “Crystal structure of the human astrovirus 2 oxford serotype capsid protein spike at 1.35-a resolution”. X-ray diffraction, 9 pockets (best druggability 0.66). MolNFT v1 #137864 on GenesisL1: 3D structure…
- PDB
- 5W1N
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid polyprotein VP90
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid polyprotein VP90 | protein | 217 | 3% helix, 47% strand | — |
| B | Capsid polyprotein VP90 | protein | 216 | 5% helix, 45% strand | — |
| C | Capsid polyprotein VP90 | protein | 213 | 3% helix, 46% strand | — |
| D | Capsid polyprotein VP90 | protein | 217 | 3% helix, 47% strand | — |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.66 | 0.77 | 54 | empty |
| 2 | 130 | 0.60 | 0.85 | 23 | empty |
| 3 | 121 | 0.60 | 0.85 | 25 | empty |
| 4 | 115 | 0.57 | 0.84 | 24 | empty |
| 5 | 98 | 0.54 | 0.84 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1976 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1944 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 269 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 112 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5W1N · Crystal structure of the human astrovirus 2 Oxford serotype capsid protein spike at… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 5W1N · PDBe 5W1N
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