MolNFT v1 · #124934 · protein
Expanded poliovirus in complex with vhh 12B
5KTZ · VP1: “Expanded poliovirus in complex with vhh 12B”. Electron microscopy, 9 pockets (best druggability 0.72). MolNFT v1 #124934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KTZ
- Type
- protein
- Length
- 805 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; Genome polyprotein; Vhh 12B
- UniProt
- P03300
- Pockets
- 9 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | VP1 | protein | 205 | 10% helix, 36% strand | P03300 |
| 2 | VP2 | protein | 246 | 13% helix, 28% strand | P03300 |
| 3 | Genome polyprotein | protein | 231 | 10% helix, 27% strand | P03300 |
| 7 | Vhh 12B | protein | 123 | 0% helix, 41% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.72 | 0.86 | 45 | empty |
| 2 | 54 | 0.62 | 0.93 | 19 | empty |
| 3 | 233 | 0.53 | 0.77 | 31 | empty |
| 4 | 286 | 0.53 | 0.75 | 50 | empty |
| 5 | 68 | 0.52 | 0.86 | 22 | empty |
Interfaces
4 interfaces between chains.
- 1–3 · 2726 Ų buried · 23 hydrogen bonds · protein-protein
- 2–3 · 1837 Ų buried · 24 hydrogen bonds · protein-protein
- 1–2 · 1271 Ų buried · 10 hydrogen bonds · protein-protein
- 3–7 · 1054 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KTZ · expanded poliovirus in complex with VHH 12B · 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 5KTZ · PDBe 5KTZ · UniProt P03300
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