MolNFT v1 · #140392 · protein
Crystal structure of HPV58 pentamer in complex with the Fab fragment of antibody A12A3
5Y9C · Major capsid protein L1: “Crystal structure of HPV58 pentamer in complex with the Fab fragment of antibody A12A3”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #140392 on GenesisL1: 3D structure, binding sites…
- 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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