MolNFT v1 · #184680 · protein
E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutations E39D F88A S247D in complex with spermidine
7OYV · Putrescine-binding periplasmic protein: “E.COLI'S putrescine receptor variant POTF/D (4JDF) with mutations E39D F88A S247D in complex with spermidine”. X-ray diffraction, 5 ligands (JFN, 3IE, SPD), 5 pockets (best druggability…
- PDB
- 7OYV
- 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
- A0A6S5NLK9
- Ligands
- JFN, 3IE, SPD, 3IZ, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putrescine-binding periplasmic protein | protein | 341 | 48% helix, 18% strand | A0A6S5NLK9 |
Ligands and binding sites
- JFN · (2R)-1-methoxypropan-2-amine · ligand · 5 copies · chains A, B
- 3IE · (2~{S})-1-methoxypropan-2-amine · ligand · 3 copies · chains A, B
- SPD · Spermidine · ligand · 2 copies · chains A, B
- 3IZ · (2~{R})-1-[(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy) propan-2-yl]oxypropan-2-yl]oxypropan-2-amine · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.77 | 0.82 | 82 | empty |
| 2 | 150 | 0.59 | 0.83 | 43 | JFN, SPD, CL |
| 3 | 140 | 0.45 | 0.76 | 28 | 3IE, CL |
| 4 | 74 | 0.38 | 0.78 | 15 | 3IE |
| 5 | 105 | 0.37 | 0.75 | 17 | JFN |
Interfaces
1 interface between chains.
- A–B · 1210 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7OYV · E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88A 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 7OYV · PDBe 7OYV · UniProt A0A6S5NLK9
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