Research workbench
Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10
Analyse Crystal structure of HPV59 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
- 5Y9F
- Type
- protein
- Length
- 8,582 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.35
- Source
- Human papillomavirus type 59; Mus musculus
- Molecule
- Major capsid protein L1; light chains of Fab fragment of antibody 28F10; heavy chain of…
- UniProt
- Q81971
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 3.35 · 9 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H, I, J | Major capsid protein L1 | protein | 420 | 11% helix, 38% strand | Q81971 |
| C, D, F | Major capsid protein L1 | protein | 421 | 11% helix, 38% strand | Q81971 |
| E | Major capsid protein L1 | protein | 427 | 11% helix, 37% strand | Q81971 |
| K, Q, M, Y, a, U | light chains of Fab fragment of antibody 28F10 | protein | 217 | 6% helix, 52% strand | — |
| L | heavy chain of Fab fragment of antibody 28F10 | protein | 222 | 4% helix, 48% strand | — |
| O, S, c | light chains of Fab fragment of antibody 28F10 | protein | 218 | 6% helix, 51% strand | — |
| P, T, N, V, X, Z, b | heavy chain of Fab fragment of antibody 28F10 | protein | 219 | 3% helix, 47% strand | — |
| R, d | heavy chain of Fab fragment of antibody 28F10 | protein | 221 | 4% helix, 48% strand | — |
| W | light chains of Fab fragment of antibody 28F10 | protein | 219 | 6% helix, 52% 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 | 866 | 0.75 | 0.79 | 83 | empty |
| 2 | 812 | 0.74 | 0.79 | 79 | empty |
| 3 | 1192 | 0.73 | 0.76 | 116 | empty |
| 4 | 522 | 0.71 | 0.81 | 67 | empty |
| 5 | 747 | 0.70 | 0.77 | 89 | empty |
Interfaces
76 interfaces between chains.
- B–E · 3667 Ų buried · 67 hydrogen bonds · protein-protein
- D–E · 3652 Ų buried · 63 hydrogen bonds · protein-protein
- F–J · 3651 Ų buried · 64 hydrogen bonds · protein-protein
- H–I · 3651 Ų buried · 58 hydrogen bonds · protein-protein
- F–G · 3623 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide (disulfide).
Compared structures
- 5Y9F · Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10 · 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 Q81971
- Elsewhere: RCSB PDB 5Y9F · PDBe 5Y9F · UniProt Q81971
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