MolNFT v1 · #176461 · protein
2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of 2H3
7DNH · Major capsid protein L1: “2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment…”. Electron microscopy, 20 pockets (best druggability 0.74). MolNFT v1 #176461 on GenesisL1: 3D…
- PDB
- 7DNH
- Type
- protein
- Length
- 2,762 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1; The light chain of 2H3 Fab fragment; The heavy chain of 2H3 Fab…
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, E | Major capsid protein L1 | protein | 472 | 9% helix, 30% strand | P26535 |
| A | Major capsid protein L1 | protein | 463 | 10% helix, 28% strand | P26535 |
| D | Major capsid protein L1 | protein | 454 | 6% helix, 32% strand | P26535 |
| L | The light chain of 2H3 Fab fragment | protein | 214 | 6% helix, 46% strand | — |
| H | The heavy chain of 2H3 Fab fragment | protein | 215 | 4% helix, 46% strand | — |
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 | 82 | 0.74 | 0.96 | 27 | empty |
| 2 | 71 | 0.73 | 0.97 | 30 | empty |
| 3 | 717 | 0.72 | 0.79 | 84 | empty |
| 4 | 109 | 0.71 | 0.93 | 23 | empty |
| 5 | 57 | 0.70 | 0.97 | 26 | empty |
Interfaces
15 interfaces between chains.
- B–C · 3869 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3744 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 3737 Ų buried · 41 hydrogen bonds · protein-protein
- B–A · 3552 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 3541 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DNH · 2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed… · the same entry in another collection · chain B against B, 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 7DNH · PDBe 7DNH · UniProt P26535
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