MolNFT v1 · #153546 · protein
The cryo-EM structure of hav bound to a neutralizing antibody-F9
6JHT · VP1: “The cryo-EM structure of hav bound to a neutralizing antibody-F9”. Electron microscopy, 11 pockets (best druggability 0.75). MolNFT v1 #153546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JHT
- Type
- protein
- Length
- 1,152 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; Fab light chain; Fab heavy chain
- Pockets
- 11 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 6% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 260 | 7% helix, 27% strand | — |
| B | VP2 | protein | 216 | 7% helix, 40% strand | — |
| C | VP3 | protein | 246 | 9% helix, 28% strand | — |
| D | Fab light chain | protein | 213 | 4% helix, 41% strand | — |
| E | Fab heavy chain | protein | 217 | 1% helix, 44% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.75 | 0.80 | 86 | empty |
| 2 | 267 | 0.57 | 0.78 | 25 | empty |
| 3 | 286 | 0.57 | 0.77 | 28 | empty |
| 4 | 333 | 0.53 | 0.74 | 50 | empty |
| 5 | 113 | 0.40 | 0.76 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3838 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2146 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1604 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1403 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 730 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6JHT · The cryo-EM structure of HAV bound to a neutralizing antibody-F9 · the same entry in another collection · chain A against A, 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 6JHT · PDBe 6JHT
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