Research workbench
C123AT mutant of E. COLI succinyl-CoA synthetase
Analyse C123AT mutant of E. COLI succinyl-CoA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NU8
- Type
- protein
- Length
- 1,347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-CoA ligase [ADP-forming] subunit alpha; Succinyl-CoA synthetase beta chain
- EC
- 6.2.1.5
- UniProt
- P0AGE9, P0A836
- Ligands
- COA, SO4, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Succinyl-CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) | protein | 287 | 36% helix, 23% strand | P0AGE9 |
| B | Succinyl-CoA synthetase beta chain (EC 6.2.1.5) | protein | 388 | 40% helix, 25% strand | P0A836 |
| E | Succinyl-CoA synthetase beta chain (EC 6.2.1.5) | protein | 385 | 40% helix, 25% strand | P0A836 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, E, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, D, E
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.81 | 0.89 | 66 | PO4 |
| 2 | 438 | 0.81 | 0.89 | 63 | empty |
| 3 | 407 | 0.80 | 0.89 | 51 | PO4, COA |
| 4 | 129 | 0.65 | 0.88 | 25 | empty |
| 5 | 84 | 0.60 | 0.88 | 21 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1909 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1896 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 956 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 227 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 226 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2NU8 · C123aT Mutant of E. coli Succinyl-CoA Synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGE9 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP- forming] subunit alpha… · a predicted model of the same protein · 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 E 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 P0AGE9
- Every structure of UniProt P0A836
- Elsewhere: RCSB PDB 2NU8 · PDBe 2NU8 · UniProt P0AGE9 · UniProt P0A836
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