MolNFT v1 · #50859 · protein
A detailed description of the structure of succinyl-CoA synthetase from escherichia COLI
2SCU · Protein (succinyl-CoA ligase): “A detailed description of the structure of succinyl-CoA synthetase from escherichia COLI”. X-ray diffraction, 2 ligands (COA, SO4), 12 pockets (best druggability 0.82). MolNFT v1 #50859 on GenesisL1…
- PDB
- 2SCU
- Type
- protein
- Length
- 1,342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (succinyl-CoA ligase)
- EC
- 6.2.1.5
- UniProt
- P07459, P07460
- Ligands
- COA, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein (succinyl-CoA ligase) (EC 6.2.1.5) | protein | 286 | 36% helix, 23% strand | P07459 |
| B, E | Protein (succinyl-CoA ligase) (EC 6.2.1.5) | protein | 385 | 40% helix, 25% strand | P07460 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, E, B, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.82 | 0.86 | 87 | empty |
| 2 | 449 | 0.79 | 0.87 | 51 | COA |
| 3 | 415 | 0.77 | 0.86 | 50 | COA |
| 4 | 265 | 0.66 | 0.83 | 37 | empty |
| 5 | 174 | 0.63 | 0.85 | 34 | SO4 |
Interfaces
5 interfaces between chains.
- D–E · 1878 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 979 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 215 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 204 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2SCU · A detailed description of the structure of Succinyl-COA synthetase from Escherichia coli · the same entry in another collection · 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 P07459
- Every structure of UniProt P07460
- Elsewhere: RCSB PDB 2SCU · PDBe 2SCU · UniProt P07459 · UniProt P07460
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