MolNFT v1 · #129179 · protein
The periplasmic binding protein component of the arabinose ABC transporter from shewanella sp. ana-3 bound to alpha and beta-L- arabinofuranose
5OCP · Periplasmic binding PROTEIN/LACI transcriptional regulator: “The periplasmic binding protein component of the arabinose ABC transporter from shewanella sp. ana-3 bound to…”. X-ray diffraction, 2 ligands (FUB, AHR), 4 pockets (best…
- PDB
- 5OCP
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- A0KWY4
- Ligands
- FUB, AHR
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 302 | 46% helix, 20% strand | A0KWY4 |
Ligands and binding sites
- FUB · beta-L-arabinofuranose · ligand · 2 copies · chains A, B
- AHR · alpha-L-arabinofuranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.74 | 0.78 | 79 | ACT |
| 2 | 282 | 0.55 | 0.76 | 38 | empty |
| 3 | 83 | 0.39 | 0.77 | 19 | empty |
| 4 | 61 | 0.36 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5OCP · The periplasmic binding protein component of the arabinose ABC transporter from… · 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 A0KWY4
- Elsewhere: RCSB PDB 5OCP · PDBe 5OCP · UniProt A0KWY4
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