Research workbench
E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutation S247D in complex with spermidine
Analyse E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutation S247D in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OYY
- Type
- protein
- Length
- 342 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine-binding periplasmic protein potf
- UniProt
- P31133
- Ligands
- SPD, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine-binding periplasmic protein potf | protein | 342 | 47% helix, 18% strand | P31133 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.70 | 0.83 | 42 | SPD, EDO, CL |
| 2 | 134 | 0.48 | 0.78 | 23 | GOL |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OYY · E.coli's putrescine receptor variant PotF/D (4JDF) with mutation S247D in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P31133 · AlphaFold monomer V2.0 prediction for putrescine-binding periplasmic protein potf (P31133) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P31133
- Elsewhere: RCSB PDB 7OYY · PDBe 7OYY · UniProt P31133
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