Research workbench
Crystal structure of a trap periplasmic solute binding protein from polaromonas sp. JS666 (BPRO_4736), target efi-510156, with bound benzoyl formate, space group P21
Analyse Crystal structure of a trap periplasmic solute binding protein from polaromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MNC
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter-dctp subunit
- UniProt
- Q122C7
- Ligands
- 173, SO4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter-dctp subunit | protein | 305 | 51% helix, 19% strand | Q122C7 |
Ligands and binding sites
- 173 · Benzoyl-formic acid · ligand · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.33 | 0.73 | 24 | empty |
| 2 | 61 | 0.27 | 0.72 | 12 | empty |
Compared structures
- 4MNC · Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666… · the same entry in another collection · chain A against A, TM-score 1.00
- Q122C7 · AlphaFold monomer V2.0 prediction for solute-binding protein BPRO_4736 (Q122C7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q122C7
- Elsewhere: RCSB PDB 4MNC · PDBe 4MNC · UniProt Q122C7
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