Research workbench
Crystal structure of a trap periplasmic solute binding protein from roseobacter denitrificans och 114 (RD1_1052, target efi-510238) with bound L-galactonate
Analyse Crystal structure of a trap periplasmic solute binding protein from roseobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PCD
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C4-dicarboxylate transport system, substrate-binding protein, putative
- UniProt
- Q16BC9
- Ligands
- 2Q2
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4-dicarboxylate transport system, substrate-binding protein, putative | protein | 300 | 52% helix, 20% strand | Q16BC9 |
Ligands and binding sites
- 2Q2 · L-galactonic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.69 | 0.96 | 24 | 2Q2 |
| 2 | 156 | 0.60 | 0.83 | 29 | empty |
| 3 | 65 | 0.35 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 4PCD · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16BC9 · AlphaFold monomer V2.0 prediction for solute-binding protein RD1_1052 (Q16BC9) · 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 Q16BC9
- Elsewhere: RCSB PDB 4PCD · PDBe 4PCD · UniProt Q16BC9
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