Research workbench
E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutations E39D F88L S247D in complex with spermidine
Analyse E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutations E39D F88L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OYW
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine-binding periplasmic protein
- UniProt
- A0A6S5NLK9
- Ligands
- 3IE, SPD, ONT, ONW, JFN, CL
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putrescine-binding periplasmic protein | protein | 348 | 47% helix, 18% strand | A0A6S5NLK9 |
Ligands and binding sites
- 3IE · (2~{S})-1-methoxypropan-2-amine · ligand · 4 copies · chains A, B
- SPD · Spermidine · ligand · 2 copies · chains A, B
- ONT · (2~{S})-1-(2-methoxyethoxy)propan-2-amine · ligand · chains A
- ONW · (2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine · ligand · chains A
- JFN · (2R)-1-methoxypropan-2-amine · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.66 | 0.96 | 22 | SPD |
| 2 | 220 | 0.61 | 0.81 | 42 | SPD, ONW, CL |
| 3 | 327 | 0.56 | 0.76 | 41 | 3IE |
| 4 | 162 | 0.47 | 0.76 | 25 | 3IE, JFN |
| 5 | 64 | 0.38 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OYW · E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L S247D in… · the same entry in another collection · chain A 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 A0A6S5NLK9
- Elsewhere: RCSB PDB 7OYW · PDBe 7OYW · UniProt A0A6S5NLK9
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