MolNFT v1 · #140394 · protein
Crystal structure of HPV58 pentamer
5Y9E · Major capsid protein L1: “Crystal structure of HPV58 pentamer”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.68). MolNFT v1 #140394 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y9E
- Type
- protein
- Length
- 2,083 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P26535
- Ligands
- MG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein L1 | protein | 416 | 16% helix, 38% strand | P26535 |
| B | Major capsid protein L1 | protein | 414 | 16% helix, 40% strand | P26535 |
| C | Major capsid protein L1 | protein | 415 | 15% helix, 39% strand | P26535 |
| D | Major capsid protein L1 | protein | 418 | 14% helix, 39% strand | P26535 |
| E | Major capsid protein L1 | protein | 420 | 15% helix, 39% strand | P26535 |
Ligands and binding sites
- MG · Magnesium ion · metal · 29 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 20 copies · chains A, C, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.68 | 0.74 | 71 | empty |
| 2 | 355 | 0.67 | 0.81 | 59 | GOL, MG |
| 3 | 340 | 0.66 | 0.81 | 59 | MG, GOL |
| 4 | 337 | 0.66 | 0.81 | 62 | GOL, MG |
| 5 | 363 | 0.65 | 0.80 | 57 | GOL, MG |
Interfaces
10 interfaces between chains.
- B–E · 3661 Ų buried · 60 hydrogen bonds · protein-protein
- D–E · 3631 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3528 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 3510 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3481 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 5Y9E · Crystal structure of HPV58 pentamer · 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 P26535
- Elsewhere: RCSB PDB 5Y9E · PDBe 5Y9E · UniProt P26535
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