MolNFT v1 · #184684 · protein
E.COLI'S putrescine receptor variant POTF/D in complex with spermidine
7OYZ · Putrescine-binding periplasmic protein potf: “E.COLI'S putrescine receptor variant POTF/D in complex with spermidine”. X-ray diffraction, 2 ligands (SPD, CL), 2 pockets (best druggability 0.69). MolNFT v1 #184684 on GenesisL1: 3D…
- PDB
- 7OYZ
- Type
- protein
- Length
- 341 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 0.69
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine-binding periplasmic protein potf | protein | 341 | 48% helix, 18% strand | P31133 |
Ligands and binding sites
- SPD · Spermidine · ligand · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · 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 | 353 | 0.69 | 0.82 | 39 | SPD, CL |
| 2 | 61 | 0.35 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OYZ · E.coli's putrescine receptor variant PotF/D in complex with spermidine · 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 7OYZ · PDBe 7OYZ · UniProt P31133
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