Research workbench
X-ray structure of mcps ligand binding domain in complex with succinate
Analyse X-ray structure of mcps ligand binding domain in complex with succinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YFB
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis transducer
- UniProt
- Q88E10
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-accepting chemotaxis transducer | protein | 235 | 90% helix, 0% strand | Q88E10 |
| B | Methyl-accepting chemotaxis transducer | protein | 238 | 91% helix, 0% strand | Q88E10 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.75 | 0.82 | 54 | ACT |
| 2 | 296 | 0.63 | 0.80 | 34 | empty |
| 3 | 67 | 0.45 | 0.82 | 15 | SIN |
| 4 | 60 | 0.42 | 0.82 | 18 | ACT |
| 5 | 67 | 0.41 | 0.80 | 19 | SIN |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2YFB · X-ray structure of McpS ligand binding domain in complex with succinate · the same entry in another collection · chain A against A, TM-score 1.00
- Q88E10 · AlphaFold monomer V2.0 prediction for methyl-accepting chemotaxis protein mcps (Q88E10) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q88E10
- Elsewhere: RCSB PDB 2YFB · PDBe 2YFB · UniProt Q88E10
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