MolNFT v1 · #16116 · protein
Crystal structure of the fosfomycin resistance protein from transposon TN2921
1NPB · Fosfomycin-resistance protein: “Crystal structure of the fosfomycin resistance protein from transposon TN2921”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.68). MolNFT v1 #16116 on GenesisL1: 3D structure…
- PDB
- 1NPB
- Type
- protein
- Length
- 830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fosfomycin-resistance protein
- UniProt
- Q56415
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fosfomycin-resistance protein | protein | 140 | 26% helix, 36% strand | Q56415 |
| B | Fosfomycin-resistance protein | protein | 139 | 24% helix, 35% strand | Q56415 |
| C, E, F | Fosfomycin-resistance protein | protein | 138 | 23% helix, 36% strand | Q56415 |
| D | Fosfomycin-resistance protein | protein | 137 | 27% helix, 36% strand | Q56415 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.68 | 0.84 | 24 | GOL |
| 2 | 272 | 0.67 | 0.83 | 25 | GOL |
| 3 | 245 | 0.66 | 0.84 | 24 | GOL |
| 4 | 330 | 0.60 | 0.78 | 35 | SO4 |
| 5 | 265 | 0.55 | 0.77 | 35 | SO4 |
Interfaces
9 interfaces between chains.
- E–F · 2639 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2633 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2618 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 480 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 468 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1NPB · Crystal structure of the fosfomycin resistance protein from transposon Tn2921 · the same entry in another collection · chain F against F, TM-score 1.00
- Q56415 · AlphaFold monomer V2.0 prediction for glutathione transferase fosa (Q56415) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q56415
- Elsewhere: RCSB PDB 1NPB · PDBe 1NPB · UniProt Q56415
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