Research workbench
immune complex of HPV6 L1 pentamer and neutralizing antibody 13H5
Analyse immune complex of HPV6 L1 pentamer and neutralizing antibody 13H5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EW5
- Type
- protein
- Length
- 8,480 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.606
- Source
- Human papillomavirus type 6; Mus musculus
- Molecule
- Major capsid protein L1; Heavy chain of 13H5; Light chain of 13H5
- UniProt
- Q9W9C6
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 3.606 · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V, Y, b | Major capsid protein L1 | protein | 416 | 14% helix, 39% strand | Q9W9C6 |
| B, E, H, K, N, g, Q, T, W, Z | Heavy chain of 13H5 | protein | 218 | 1% helix, 45% strand | — |
| C, F, I, L, O, j, R, U, X, a | Light chain of 13H5 | protein | 214 | 5% helix, 50% 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 | 752 | 0.82 | 0.86 | 97 | empty |
| 2 | 458 | 0.82 | 0.89 | 58 | empty |
| 3 | 1018 | 0.82 | 0.83 | 125 | empty |
| 4 | 686 | 0.81 | 0.86 | 88 | empty |
| 5 | 402 | 0.81 | 0.90 | 52 | empty |
Interfaces
99 interfaces between chains.
- P–S · 3602 Ų buried · 60 hydrogen bonds · protein-protein
- G–J · 3594 Ų buried · 64 hydrogen bonds · protein-protein
- Y–b · 3593 Ų buried · 61 hydrogen bonds · protein-protein
- A–M · 3592 Ų buried · 66 hydrogen bonds · protein-protein
- V–Y · 3587 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
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 Q9W9C6
- Elsewhere: RCSB PDB 7EW5 · PDBe 7EW5 · UniProt Q9W9C6
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