Research workbench
Crystal structure analysis of the E197BETAA mutant of E. COLI scs
Analyse Crystal structure analysis of the E197BETAA mutant of E. COLI scs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JLL
- Type
- protein
- Length
- 1,347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-CoA synthetase alpha subunit; Succinyl-CoA synthetase beta subunit
- EC
- 6.2.1.5
- UniProt
- P07459, P0A836
- Ligands
- COA, SO4, PO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Succinyl-CoA synthetase alpha subunit (EC 6.2.1.5) | protein | 287 | 35% helix, 22% strand | P07459 |
| B | Succinyl-CoA synthetase beta subunit (EC 6.2.1.5) | protein | 388 | 39% helix, 23% strand | P0A836 |
| E | Succinyl-CoA synthetase beta subunit (EC 6.2.1.5) | protein | 385 | 39% helix, 24% strand | P0A836 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, E, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains B, A, E, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.78 | 0.89 | 56 | PO4, COA |
| 2 | 269 | 0.77 | 0.90 | 56 | PO4, COA |
| 3 | 182 | 0.70 | 0.88 | 32 | empty |
| 4 | 133 | 0.68 | 0.89 | 19 | empty |
| 5 | 136 | 0.67 | 0.89 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1880 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1874 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 984 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 232 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1JLL · Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS · the same entry in another collection · chain E against E, TM-score 1.00
- P0A836 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP- forming] subunit beta… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P07459
- Every structure of UniProt P0A836
- Elsewhere: RCSB PDB 1JLL · PDBe 1JLL · UniProt P07459 · UniProt P0A836
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