Research workbench
Pseudo-atomic structure of human papillomavirus type 59 L1 virus-like particle
Analyse Pseudo-atomic structure of human papillomavirus type 59 L1 virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JB1
- Type
- protein
- Length
- 2,749 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- Q81971
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein L1 | protein | 456 | 13% helix, 33% strand | Q81971 |
| B, F | Major capsid protein L1 | protein | 464 | 12% helix, 33% strand | Q81971 |
| C | Major capsid protein L1 | protein | 457 | 12% helix, 33% strand | Q81971 |
| D, E | Major capsid protein L1 | protein | 454 | 12% helix, 32% strand | Q81971 |
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 | 342 | 0.86 | 0.95 | 84 | empty |
| 2 | 279 | 0.85 | 0.95 | 75 | empty |
| 3 | 281 | 0.84 | 0.95 | 77 | empty |
| 4 | 272 | 0.84 | 0.95 | 84 | empty |
| 5 | 224 | 0.82 | 0.95 | 51 | empty |
Interfaces
12 interfaces between chains.
- B–C · 2945 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 2894 Ų buried · 77 hydrogen bonds · protein-protein
- A–E · 2841 Ų buried · 71 hydrogen bonds · protein-protein
- D–E · 2774 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 2739 Ų buried · 62 hydrogen bonds · protein-protein
Compared structures
- 5JB1 · Pseudo-atomic structure of Human Papillomavirus Type 59 L1 Virus-like Particle · 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 Q81971
- Elsewhere: RCSB PDB 5JB1 · PDBe 5JB1 · UniProt Q81971
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