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Crystal structure of MG2+ / BEF3-bound receiver domain of sinorhizobium meliloti dctd
Analyse Crystal structure of MG2+ / BEF3-bound receiver domain of sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L5Y
- Type
- protein
- Length
- 294 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Sinorhizobium meliloti
- Molecule
- C4-dicarboxylate transport transcriptional regulatory protein dctd
- UniProt
- P13632
- Ligands
- BF2, BEF, BF4, MG, SO4
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4-dicarboxylate transport transcriptional regulatory protein dctd | protein | 143 | 48% helix, 17% strand | P13632 |
| B | C4-dicarboxylate transport transcriptional regulatory protein dctd | protein | 151 | 53% helix, 16% strand | P13632 |
Ligands and binding sites
- BF2 · Beryllium difluoride · ligand · 10 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B
- BF4 · Beryllium tetrafluoride ion · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1L5Y · Crystal structure of MG2+ / BEF3-bound receiver domain of sinorhizobium meliloti dctd · the same entry in another collection · chain A against A, TM-score 1.00
- P13632 · AlphaFold monomer V2.0 prediction for C4-dicarboxylate transport transcriptional… · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P13632
- Elsewhere: RCSB PDB 1L5Y · PDBe 1L5Y · UniProt P13632
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