MolNFT v1 · #175324 · protein
Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
7CN2 · The light chain variable region of H16.001 Fab fragment: “Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #175324…
- 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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