MolNFT v1 · #153543 · protein
The cryo-EM structure of hav bound to a neutralizing antibody-F4
6JHQ · VP1: “The cryo-EM structure of hav bound to a neutralizing antibody-F4”. Electron microscopy, 11 pockets (best druggability 0.77). MolNFT v1 #153543 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JHQ
- Type
- protein
- Length
- 1,152 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; Fab heavy chain; Fab light chain
- Pockets
- 11 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 260 | 9% helix, 27% strand | — |
| B | VP2 | protein | 216 | 9% helix, 37% strand | — |
| C | VP3 | protein | 246 | 6% helix, 35% strand | — |
| D | Fab heavy chain | protein | 217 | 4% helix, 46% strand | — |
| E | Fab light chain | protein | 213 | 4% helix, 48% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.77 | 0.81 | 71 | empty |
| 2 | 229 | 0.56 | 0.79 | 35 | empty |
| 3 | 256 | 0.56 | 0.77 | 26 | empty |
| 4 | 122 | 0.40 | 0.75 | 20 | empty |
| 5 | 141 | 0.38 | 0.73 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3855 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 2042 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1249 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 960 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6JHQ · The cryo-EM structure of HAV bound to a neutralizing antibody-F4 · the same entry in another collection · chain D against D, 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 6JHQ · PDBe 6JHQ
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