Research workbench
2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of 5G9
Analyse 2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DNK
- Type
- protein
- Length
- 2,761 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The light chain of 5G9 Fab fragment; The heavy chain of 5G9 Fab fragment; Major capsid…
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 5 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | The light chain of 5G9 Fab fragment | protein | 214 | 5% helix, 44% strand | — |
| H | The heavy chain of 5G9 Fab fragment | protein | 214 | 3% helix, 43% strand | — |
| B, C, E | Major capsid protein L1 | protein | 472 | 9% helix, 27% strand | P26535 |
| A | Major capsid protein L1 | protein | 463 | 9% helix, 27% strand | P26535 |
| D | Major capsid protein L1 | protein | 454 | 10% helix, 27% strand | P26535 |
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 | 1005 | 0.91 | 0.94 | 164 | empty |
| 2 | 1044 | 0.91 | 0.93 | 178 | empty |
| 3 | 588 | 0.89 | 0.94 | 106 | empty |
| 4 | 703 | 0.84 | 0.88 | 109 | empty |
| 5 | 360 | 0.83 | 0.92 | 68 | empty |
Interfaces
18 interfaces between chains.
- A–E · 3504 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 3297 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3179 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 3035 Ų buried · 53 hydrogen bonds · protein-protein
- B–A · 2975 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DNK · 2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed… · 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 P26535
- Elsewhere: RCSB PDB 7DNK · PDBe 7DNK · UniProt P26535
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