Research workbench
E.COLI'S putrescine receptor potf in its open apo state
Analyse E.COLI'S putrescine receptor potf in its open apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YED
- 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
- CL
- Pockets
- 2 · best druggability 0.71
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 | P31133 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.71 | 0.75 | 119 | PGE, EDO, CL |
| 2 | 352 | 0.56 | 0.75 | 39 | PEG, EDO, CL |
Interfaces
1 interface between chains.
- A–B · 339 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YED · E.coli's Putrescine receptor PotF in its open 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 0.78
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 6YED · PDBe 6YED · UniProt P31133
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.