MolNFT v1 · #145275 · protein
Structure of the poxvirus protein F9
6CJ6: “Structure of the poxvirus protein F9”. X-ray diffraction, 2 ligands (ETX, ETE), 9 pockets (best druggability 0.74). MolNFT v1 #145275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CJ6
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein F9
- UniProt
- P24361
- Ligands
- ETX, ETE
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein F9 | protein | 165 | 41% helix, 23% strand | P24361 |
| B | Protein F9 | protein | 161 | 42% helix, 24% strand | P24361 |
| C | Protein F9 | protein | 161 | 42% helix, 25% strand | P24361 |
| D | Protein F9 | protein | 166 | 40% helix, 24% strand | P24361 |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · 8 copies · chains A, B, C, D
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · 2 copies · chains B, D, C
- EOH · Ethanol · additive · 47 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, C, D, B
- MOH · Methanol · additive · 25 copies · chains A, D, C, B
- PDO · 1,3-propandiol · additive · 14 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, C, B, D
- PGO · S-1,2-propanediol · additive · 10 copies · chains A, C, B, D
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 9 copies · chains A, D, B, C
- GOL · Glycerol · additive · 6 copies · chains A, C, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, D
- PGE · Triethylene glycol · additive · 5 copies · chains B, C, A, D
- P6G · Hexaethylene glycol · additive · 3 copies · chains D
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.74 | 0.77 | 80 | PG0, GOL, MOH, PDO, PEG, PGO, EDO |
| 2 | 85 | 0.40 | 0.78 | 17 | empty |
| 3 | 109 | 0.38 | 0.75 | 22 | EDO, MOH |
| 4 | 92 | 0.37 | 0.76 | 18 | empty |
| 5 | 75 | 0.36 | 0.77 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 821 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 575 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6CJ6 · Structure of the poxvirus protein F9 · 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 P24361
- Elsewhere: RCSB PDB 6CJ6 · PDBe 6CJ6 · UniProt P24361
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