Research workbench
E.COLI'S putrescine receptor potf complexed with spermidine
Analyse E.COLI'S putrescine receptor potf complexed with spermidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YE8
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine-binding periplasmic protein
- UniProt
- P31133
- Ligands
- JFN, SPD, ONT, CL, SO4
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine-binding periplasmic protein | protein | 342 | 48% helix, 18% strand | P31133 |
| B | Putrescine-binding periplasmic protein | protein | 340 | 49% helix, 18% strand | P31133 |
Ligands and binding sites
- JFN · (2R)-1-methoxypropan-2-amine · ligand · 7 copies · chains A, B
- SPD · Spermidine · ligand · 2 copies · chains A, B
- ONT · (2~{S})-1-(2-methoxyethoxy)propan-2-amine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.49 | 0.75 | 40 | empty |
| 2 | 142 | 0.46 | 0.77 | 19 | ONT |
| 3 | 137 | 0.42 | 0.75 | 21 | ONT |
Interfaces
1 interface between chains.
- A–B · 293 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YE8 · E.coli's Putrescine receptor PotF complexed 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 B 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 P31133
- Elsewhere: RCSB PDB 6YE8 · PDBe 6YE8 · UniProt P31133
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