Research workbench
The crystal structure of succinyl-CoA synthetase from escherichia COLI at 2.5 ångströms resolution
Analyse The crystal structure of succinyl-CoA synthetase from escherichia COLI at 2.5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SCU
- Type
- protein
- Length
- 1,352 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
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Succinyl-CoA synthetase, alpha subunit (EC 6.2.1.5) | protein | 288 | 37% helix, 23% strand | P07459 |
| B, E | Succinyl-CoA synthetase, beta subunit (EC 6.2.1.5) | protein | 388 | 42% helix, 24% strand | P0A836 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, E, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.84 | 0.86 | 105 | COA |
| 2 | 404 | 0.76 | 0.86 | 52 | COA |
| 3 | 265 | 0.71 | 0.86 | 38 | empty |
| 4 | 138 | 0.64 | 0.87 | 22 | empty |
| 5 | 117 | 0.61 | 0.86 | 24 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1827 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1772 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 978 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 202 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 199 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1SCU · The crystal structure of succinyl-CoA synthetase from escherichia COLI at 2.5 ångströms… · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.98
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 1SCU · PDBe 1SCU · UniProt P07459 · UniProt P0A836
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