MolNFT v1 · #149976 · protein
Cryo-EM structure of bk polyomavirus like particle in complex with single chain antibody SCFV41F17
6GG0 · Capsid protein VP1: “Cryo-EM structure of bk polyomavirus like particle in complex with single chain antibody SCFV41F17”. Electron microscopy, 20 pockets (best druggability 0.78). MolNFT v1 #149976 on GenesisL1: 3D structure…
- PDB
- 6GG0
- Type
- protein
- Length
- 2,269 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Heavy chain; Light chain
- UniProt
- Q65613
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 8 distinct chains · 6% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 347 | 5% helix, 25% strand | Q65613 |
| 2 | Capsid protein VP1 | protein | 346 | 6% helix, 31% strand | Q65613 |
| 3 | Capsid protein VP1 | protein | 343 | 7% helix, 27% strand | Q65613 |
| 4 | Capsid protein VP1 | protein | 318 | 9% helix, 24% strand | Q65613 |
| 5 | Capsid protein VP1 | protein | 338 | 9% helix, 25% strand | Q65613 |
| 6 | Capsid protein VP1 | protein | 345 | 5% helix, 30% strand | Q65613 |
| H | Heavy chain | protein | 123 | 5% helix, 39% strand | — |
| L | Light chain | protein | 109 | 0% helix, 38% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.78 | 0.80 | 129 | empty |
| 2 | 541 | 0.78 | 0.85 | 43 | empty |
| 3 | 971 | 0.76 | 0.79 | 78 | empty |
| 4 | 1161 | 0.73 | 0.77 | 110 | empty |
| 5 | 1159 | 0.73 | 0.76 | 93 | empty |
Interfaces
11 interfaces between chains.
- 2–3 · 3114 Ų buried · 26 hydrogen bonds · protein-protein
- 4–5 · 2766 Ų buried · 32 hydrogen bonds · protein-protein
- 1–2 · 2712 Ų buried · 33 hydrogen bonds · protein-protein
- 3–4 · 2618 Ų buried · 32 hydrogen bonds · protein-protein
- 1–5 · 2498 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6GG0 · Cryo-EM structure of BK polyomavirus like particle in complex with single chain antibody… · 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 Q65613
- Elsewhere: RCSB PDB 6GG0 · PDBe 6GG0 · UniProt Q65613
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