Research workbench
Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab
Analyse Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J8Z
- Type
- protein
- Length
- 3,021 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L1; H16.1A light chain; H16.1A heavy chain
- UniProt
- Q4VRM0
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 12% helix, 42% 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 | H16.1A light chain | protein | 115 | 3% helix, 50% strand | — |
| H, F, G, I | H16.1A heavy chain | protein | 114 | 11% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.80 | 0.88 | 71 | empty |
| 2 | 782 | 0.79 | 0.83 | 102 | empty |
| 3 | 820 | 0.77 | 0.81 | 115 | empty |
| 4 | 823 | 0.76 | 0.80 | 105 | empty |
| 5 | 888 | 0.67 | 0.74 | 62 | empty |
Interfaces
32 interfaces between chains.
- B–C · 3480 Ų buried · 62 hydrogen bonds · protein-protein
- A–E · 3468 Ų buried · 66 hydrogen bonds · protein-protein
- D–E · 3466 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3464 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3454 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3J8Z · Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A 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 3J8Z · PDBe 3J8Z · UniProt Q4VRM0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.