Research workbench
Crystal structure of a trap periplasmic solute binding protein from ruegeria pomeroyi dss-3 (SPO1773, target efi-510260) with bound benzoic acid
Analyse Crystal structure of a trap periplasmic solute binding protein from ruegeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PBH
- Type
- protein
- Length
- 308 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit, putative
- UniProt
- Q5LSJ5
- Ligands
- BEZ
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit, putative | protein | 308 | 52% helix, 18% strand | Q5LSJ5 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.65 | 0.90 | 27 | BEZ |
| 2 | 50 | 0.27 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4PBH · Crystal structure of a trap periplasmic solute binding protein from ruegeria pomeroyi… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5LSJ5 · AlphaFold monomer V2.0 prediction for solute-binding protein SPO1773 (Q5LSJ5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5LSJ5
- Elsewhere: RCSB PDB 4PBH · PDBe 4PBH · UniProt Q5LSJ5
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