Research workbench
The cryo-EM structure of human papillomavirus type 58 pseudovirus
Analyse The cryo-EM structure of human papillomavirus type 58 pseudovirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DN5
- Type
- protein
- Length
- 2,787 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 8% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, E | Major capsid protein L1 | protein | 472 | 8% helix, 24% strand | P26535 |
| A | Major capsid protein L1 | protein | 463 | 8% helix, 25% strand | P26535 |
| D, F | Major capsid protein L1 | protein | 454 | 7% helix, 29% strand | P26535 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.78 | 0.80 | 126 | empty |
| 2 | 55 | 0.69 | 0.97 | 24 | empty |
| 3 | 615 | 0.69 | 0.77 | 76 | empty |
| 4 | 51 | 0.69 | 0.98 | 19 | empty |
| 5 | 545 | 0.66 | 0.77 | 66 | empty |
Interfaces
12 interfaces between chains.
- B–C · 3863 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 3789 Ų buried · 26 hydrogen bonds · protein-protein
- B–A · 3743 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 3665 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 3629 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7DN5 · The cryo-EM structure of human papillomavirus type 58 pseudovirus · the same entry in another collection · chain C against C, 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 P26535
- Elsewhere: RCSB PDB 7DN5 · PDBe 7DN5 · UniProt P26535
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.