MolNFT v1 · #170652 · protein
E.COLI'S putrescine receptor potf in its closed apo state
6YEB · Putrescine-binding periplasmic protein: “E.COLI'S putrescine receptor potf in its closed apo state”. X-ray diffraction, 2 ligands (SO4, CL), 5 pockets (best druggability 0.78). MolNFT v1 #170652 on GenesisL1: 3D structure, binding…
- PDB
- 6YEB
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine-binding periplasmic protein
- UniProt
- P31133
- Ligands
- SO4, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine-binding periplasmic protein | protein | 341 | 49% helix, 18% strand | P31133 |
| B | Putrescine-binding periplasmic protein | protein | 340 | 50% helix, 18% strand | P31133 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.78 | 0.82 | 72 | CL, EDO, PEG |
| 2 | 124 | 0.46 | 0.77 | 21 | PEG, EDO |
| 3 | 114 | 0.39 | 0.74 | 21 | PEG, EDO |
| 4 | 63 | 0.29 | 0.74 | 14 | SO4 |
| 5 | 57 | 0.29 | 0.75 | 11 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6YEB · E.coli's Putrescine receptor PotF in its closed apo state · 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 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 6YEB · PDBe 6YEB · UniProt P31133
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