Research workbench
Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
Analyse Subparticle refinement of human papillomavirus type 16 pesudovirus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CN2
- Type
- protein
- Length
- 4,233 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The light chain variable region of H16.001 Fab fragment; The heavy chain variable region…
- UniProt
- P03101
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| g, i, j, k, m, L | The light chain variable region of H16.001 Fab fragment | protein | 110 | 0% helix, 34% strand | — |
| G, I, J, K, M, H | The heavy chain variable region of H16.001 Fab fragment | protein | 120 | 3% helix, 44% strand | — |
| A | Major capsid protein L1 | protein | 474 | 8% helix, 24% strand | P03101 |
| B | Major capsid protein L1 | protein | 466 | 11% helix, 34% strand | P03101 |
| C | Major capsid protein L1 | protein | 479 | 8% helix, 30% strand | P03101 |
| D, E, F | Major capsid protein L1 | protein | 478 | 9% helix, 30% strand | P03101 |
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 | 729 | 0.79 | 0.83 | 103 | empty |
| 2 | 998 | 0.75 | 0.78 | 115 | empty |
| 3 | 763 | 0.74 | 0.80 | 97 | empty |
| 4 | 829 | 0.74 | 0.79 | 97 | empty |
| 5 | 1101 | 0.72 | 0.76 | 120 | empty |
Interfaces
50 interfaces between chains.
- C–D · 4107 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4061 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 4047 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 3973 Ų buried · 41 hydrogen bonds · protein-protein
- B–F · 3846 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7CN2 · Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with… · the same entry in another collection · chain g against g, 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 P03101
- Elsewhere: RCSB PDB 7CN2 · PDBe 7CN2 · UniProt P03101
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