Research workbench
Crystal structure of a trap periplasmic solute binding protein from chromohalobacter salexigens dsm 3043 (CSAL_2479), target efi-510085, with bound D-glucuronate, spg I213
Analyse Crystal structure of a trap periplasmic solute binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P1L
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap dicarboxylate transporter, dctp subunit
- UniProt
- Q1QUN2
- Ligands
- BDP, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap dicarboxylate transporter, dctp subunit | protein | 302 | 51% helix, 18% strand | Q1QUN2 |
| B | Trap dicarboxylate transporter, dctp subunit | protein | 301 | 52% helix, 18% strand | Q1QUN2 |
Ligands and binding sites
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.72 | 0.82 | 64 | BDP |
| 2 | 98 | 0.62 | 0.89 | 26 | BDP |
| 3 | 136 | 0.44 | 0.76 | 31 | empty |
| 4 | 70 | 0.38 | 0.79 | 18 | empty |
| 5 | 90 | 0.38 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 580 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4P1L · Crystal structure of a trap periplasmic solute binding protein from chromohalobacter… · the same entry in another collection · chain A against A, TM-score 1.00
- Q1QUN2 · AlphaFold monomer V2.0 prediction for solute-binding protein CSAL_2479 (Q1QUN2) · 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 Q1QUN2
- Elsewhere: RCSB PDB 4P1L · PDBe 4P1L · UniProt Q1QUN2
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