MolNFT v1 · #125025 · protein
Expanded poliovirus in complex with vhh 10E
5KWL · VP1: “Expanded poliovirus in complex with vhh 10E”. Electron microscopy, 10 pockets (best druggability 0.61). MolNFT v1 #125025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KWL
- Type
- protein
- Length
- 785 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; Vhh 10E
- UniProt
- P03300
- Pockets
- 10 · best druggability 0.61
Structure
electron microscopy · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | VP1 | protein | 190 | 10% helix, 37% strand | P03300 |
| 2 | VP2 | protein | 241 | 12% helix, 32% strand | P03300 |
| 3 | VP3 | protein | 230 | 10% helix, 25% strand | P03300 |
| 7 | Vhh 10E | protein | 124 | 0% helix, 40% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.61 | 0.88 | 29 | empty |
| 2 | 201 | 0.56 | 0.79 | 27 | empty |
| 3 | 292 | 0.54 | 0.75 | 45 | empty |
| 4 | 73 | 0.48 | 0.83 | 21 | empty |
| 5 | 55 | 0.47 | 0.85 | 18 | empty |
Interfaces
4 interfaces between chains.
- 1–3 · 2064 Ų buried · 25 hydrogen bonds · protein-protein
- 2–3 · 1773 Ų buried · 22 hydrogen bonds · protein-protein
- 1–2 · 1264 Ų buried · 15 hydrogen bonds · protein-protein
- 3–7 · 1083 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KWL · expanded poliovirus in complex with VHH 10E · the same entry in another collection · chain 1 against 1, 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 P03300
- Elsewhere: RCSB PDB 5KWL · PDBe 5KWL · UniProt P03300
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