MolNFT v1 · #68117 · protein
Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab
3J8V · L1: “Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #68117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3J8V
- Type
- protein
- Length
- 3,017 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L1; H16.14J light chain; H16.14J heavy chain
- UniProt
- Q4VRM0
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | L1 | protein | 421 | 14% helix, 38% strand | Q4VRM0 |
| L, J, K, M | H16.14J light chain | protein | 109 | 3% helix, 48% strand | — |
| H, F, G, I | H16.14J heavy chain | protein | 119 | 8% helix, 58% strand | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.82 | 0.84 | 97 | empty |
| 2 | 1016 | 0.81 | 0.82 | 97 | empty |
| 3 | 1105 | 0.81 | 0.82 | 102 | empty |
| 4 | 1123 | 0.81 | 0.82 | 114 | empty |
| 5 | 860 | 0.67 | 0.74 | 51 | empty |
Interfaces
33 interfaces between chains.
- B–C · 3480 Ų buried · 62 hydrogen bonds · protein-protein
- A–E · 3470 Ų buried · 66 hydrogen bonds · protein-protein
- D–E · 3464 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3463 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3454 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3J8V · Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab · 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
- Every structure of UniProt Q4VRM0
- Elsewhere: RCSB PDB 3J8V · PDBe 3J8V · UniProt Q4VRM0
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