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Crystal structure of the complex of ADP and MG2+ with dephosphorylated E. COLI succinyl-CoA synthetase
Analyse Crystal structure of the complex of ADP and MG2+ with dephosphorylated E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CQI
- Type
- protein
- Length
- 1,342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (succinyl-CoA synthetase alpha chain); Protein (succinyl-CoA synthetase beta…
- EC
- 6.2.1.5
- UniProt
- P07459, P07460
- Ligands
- COA, ADP, MG, PO4
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein (succinyl-CoA synthetase alpha chain) (EC 6.2.1.5) | protein | 286 | 34% helix, 23% strand | P07459 |
| B, E | Protein (succinyl-CoA synthetase beta chain) (EC 6.2.1.5) | protein | 385 | 40% helix, 26% strand | P07460 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, E, B, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains B, E
- 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
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.75 | 0.88 | 44 | empty |
| 2 | 208 | 0.74 | 0.90 | 57 | PO4 |
| 3 | 186 | 0.71 | 0.88 | 41 | COA |
| 4 | 198 | 0.68 | 0.86 | 34 | empty |
| 5 | 188 | 0.66 | 0.86 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1881 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1871 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1036 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 218 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 192 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1CQI · Crystal Structure of the Complex of ADP and MG2+ with Dephosphorylated E. 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 1CQI · PDBe 1CQI · UniProt P07459 · UniProt P07460
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