Research workbench
2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of A4B4
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
- 7DNL
- Type
- protein
- Length
- 2,769 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The light chain of A4B4 Fab fragment; The heavy chain of 2H3 Fab fragment; Major capsid…
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 5 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | The light chain of A4B4 Fab fragment | protein | 220 | 4% helix, 47% strand | — |
| H | The heavy chain of 2H3 Fab fragment | protein | 216 | 1% helix, 38% strand | — |
| B, C, E | Major capsid protein L1 | protein | 472 | 10% helix, 31% strand | P26535 |
| A | Major capsid protein L1 | protein | 463 | 11% helix, 30% strand | P26535 |
| D | Major capsid protein L1 | protein | 454 | 11% helix, 31% 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 | 64 | 0.71 | 0.97 | 24 | empty |
| 2 | 67 | 0.71 | 0.96 | 23 | empty |
| 3 | 1003 | 0.70 | 0.74 | 80 | empty |
| 4 | 460 | 0.70 | 0.80 | 57 | empty |
| 5 | 55 | 0.68 | 0.97 | 23 | empty |
Interfaces
15 interfaces between chains.
- B–C · 3866 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 3733 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3721 Ų buried · 42 hydrogen bonds · protein-protein
- B–A · 3658 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3594 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7DNL · 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 7DNL · PDBe 7DNL · UniProt P26535
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