MolNFT v1 · #188228 · protein
Cryo-EM structure of W6 possum enterovirus
7THX · Capsid protein VP1: “Cryo-EM structure of W6 possum enterovirus”. Electron microscopy, 2 ligands (SPH, K), 14 pockets (best druggability 0.87). MolNFT v1 #188228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7THX
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- Ligands
- SPH, K
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 265 | 12% helix, 33% strand | — |
| 2 | Capsid protein VP2 | protein | 236 | 14% helix, 39% strand | — |
| 3 | Capsid protein VP3 | protein | 235 | 10% helix, 31% strand | — |
| 4 | Capsid protein VP4 | protein | 40 | 18% helix, 8% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.87 | 0.92 | 61 | SPH |
| 2 | 241 | 0.59 | 0.80 | 29 | empty |
| 3 | 62 | 0.58 | 0.90 | 19 | empty |
| 4 | 169 | 0.51 | 0.78 | 42 | empty |
| 5 | 161 | 0.51 | 0.79 | 26 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 3608 Ų buried · 55 hydrogen bonds · protein-protein
- 1–2 · 1957 Ų buried · 26 hydrogen bonds · protein-protein
- 2–3 · 1653 Ų buried · 15 hydrogen bonds · protein-protein
- 1–4 · 1187 Ų buried · 21 hydrogen bonds · protein-protein
- 3–4 · 972 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7THX · Cryo-EM structure of W6 possum enterovirus · the same entry in another collection · chain 2 against 2, 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 7THX · PDBe 7THX
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