Research workbench
The U4 antibody epitope on human papillomavirus 16 identified by cryo- EM
Analyse The U4 antibody epitope on human papillomavirus 16 identified by cryo- EM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBA
- Type
- protein
- Length
- 3,098 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H16.U4 antibody light chain; H16.U4 antibody heavy chain; Major capsid protein L1
- UniProt
- C9E771
- Pockets
- 20 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | H16.U4 antibody light chain | protein | 115 | 3% helix, 52% strand | — |
| H | H16.U4 antibody heavy chain | protein | 115 | 5% helix, 52% strand | — |
| B, A, E, D, C, F | Major capsid protein L1 | protein | 478 | 9% helix, 31% strand | C9E771 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.69 | 0.83 | 80 | empty |
| 2 | 701 | 0.66 | 0.76 | 79 | empty |
| 3 | 283 | 0.66 | 0.83 | 61 | empty |
| 4 | 294 | 0.65 | 0.82 | 68 | empty |
| 5 | 382 | 0.65 | 0.80 | 67 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1260 Ų buried · 29 hydrogen bonds · protein-protein
- D–C · 1210 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1156 Ų buried · 18 hydrogen bonds · protein-protein
- E–D · 1094 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 1044 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3JBA · The U4 antibody epitope on human papillomavirus 16 identified by cryo-EM · the same entry in another collection · chain L against L, 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 C9E771
- Elsewhere: RCSB PDB 3JBA · PDBe 3JBA · UniProt C9E771
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