MolNFT v1 · #142305 · protein
Salmonella typhi yfdx in the P222 space group
6A09 · Yfdx protein: “Salmonella typhi yfdx in the P222 space group”. X-ray diffraction, 20 pockets (best druggability 0.65). MolNFT v1 #142305 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A09
- Type
- protein
- Length
- 1,374 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfdx protein
- UniProt
- A0A0F7DJF1
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfdx protein | protein | 174 | 53% helix, 20% strand | A0A0F7DJF1 |
| B, D, E, F | Yfdx protein | protein | 172 | 54% helix, 23% strand | A0A0F7DJF1 |
| C, G | Yfdx protein | protein | 171 | 54% helix, 23% strand | A0A0F7DJF1 |
| H | Yfdx protein | protein | 170 | 55% helix, 19% strand | A0A0F7DJF1 |
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.65 | 0.77 | 44 | empty |
| 2 | 373 | 0.58 | 0.76 | 57 | empty |
| 3 | 89 | 0.54 | 0.85 | 42 | empty |
| 4 | 260 | 0.49 | 0.74 | 34 | empty |
| 5 | 123 | 0.45 | 0.78 | 22 | empty |
Interfaces
8 interfaces between chains.
- E–G · 1870 Ų buried · 21 hydrogen bonds · protein-protein
- F–H · 1197 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1186 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1128 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 328 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6A09 · Salmonella Typhi YfdX in the P222 space group · 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 A0A0F7DJF1
- Elsewhere: RCSB PDB 6A09 · PDBe 6A09 · UniProt A0A0F7DJF1
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