Research workbench
Crystal structure of HPV58 pentamer in complex with the Fab fragment of antibody A12A3
Analyse Crystal structure of HPV58 pentamer in complex with the Fab fragment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9C
- Type
- protein
- Length
- 2,493 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1; Heavy chain of Fab fragment of antibody A12A3; Light chain of…
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein L1 | protein | 417 | 15% helix, 38% strand | P26535 |
| B | Major capsid protein L1 | protein | 420 | 15% helix, 40% strand | P26535 |
| C | Major capsid protein L1 | protein | 415 | 15% helix, 38% strand | P26535 |
| D, E | Major capsid protein L1 | protein | 414 | 16% helix, 39% strand | P26535 |
| H | Heavy chain of Fab fragment of antibody A12A3 | protein | 210 | 1% helix, 48% strand | — |
| L | Light chain of Fab fragment of antibody A12A3 | protein | 203 | 4% helix, 45% strand | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.71 | 0.83 | 51 | empty |
| 2 | 371 | 0.68 | 0.81 | 48 | empty |
| 3 | 716 | 0.67 | 0.76 | 44 | empty |
| 4 | 349 | 0.67 | 0.81 | 59 | empty |
| 5 | 330 | 0.65 | 0.81 | 52 | empty |
Interfaces
18 interfaces between chains.
- B–E · 3638 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3634 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 3603 Ų buried · 54 hydrogen bonds · protein-protein
- D–E · 3572 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3543 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5Y9C · Crystal structure of HPV58 pentamer in complex with the Fab fragment of antibody A12A3 · 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 5Y9C · PDBe 5Y9C · UniProt P26535
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