MolNFT v1 · #124420 · protein
High resolution cryo-EM maps of human papillomavirus 16 reveal L2 location and heparin-induced conformational changes
5KEP · Major capsid protein L1: “High resolution cryo-EM maps of human papillomavirus 16 reveal L2 location and heparin-induced conformational…”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #124420 on GenesisL1: 3D…
- PDB
- 5KEP
- Type
- protein
- Length
- 2,835 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P03101
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 6 distinct chains · 12% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein L1 | protein | 474 | 10% helix, 27% strand | P03101 |
| B | Major capsid protein L1 | protein | 463 | 13% helix, 30% strand | P03101 |
| C | Major capsid protein L1 | protein | 472 | 12% helix, 29% strand | P03101 |
| D | Major capsid protein L1 | protein | 471 | 12% helix, 31% strand | P03101 |
| E | Major capsid protein L1 | protein | 482 | 12% helix, 30% strand | P03101 |
| F | Major capsid protein L1 | protein | 473 | 11% helix, 30% strand | P03101 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.75 | 0.79 | 110 | empty |
| 2 | 793 | 0.75 | 0.79 | 77 | empty |
| 3 | 625 | 0.74 | 0.80 | 64 | empty |
| 4 | 540 | 0.73 | 0.81 | 69 | empty |
| 5 | 499 | 0.73 | 0.82 | 56 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4094 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 4040 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 3877 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3845 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 3736 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5KEP · High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and… · the same entry in another collection · chain A against A, 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 5KEP · PDBe 5KEP · UniProt P03101
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