MolNFT v1 · #115128 · protein
Succinate bound to pig GTP-specific succinyl-CoA synthetase
5CAE · Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha…: “Succinate bound to pig GTP-specific succinyl-CoA synthetase”. X-ray diffraction, 4 ligands (COA, MG, CL), 6 pockets (best druggability 0.78). MolNFT v1 #115128 on GenesisL1: 3D…
- PDB
- 5CAE
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial; Succinyl-CoA ligase…
- EC
- 6.2.1.4, 6.2.1.5
- UniProt
- O19069, P53590
- Ligands
- COA, MG, CL, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial (EC 6.2.1.4, 6.2.1.5) | protein | 303 | 38% helix, 22% strand | O19069 |
| B | Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 393 | 38% helix, 25% strand | P53590 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- SIN · Succinic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.78 | 0.82 | 62 | empty |
| 2 | 230 | 0.71 | 0.87 | 35 | PO4, MG, SIN |
| 3 | 168 | 0.57 | 0.82 | 26 | GOL |
| 4 | 156 | 0.47 | 0.77 | 19 | empty |
| 5 | 53 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2307 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5CAE · Succinate bound to pig GTP-specific succinyl-CoA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- O19069 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP/GDP- forming] subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P53590 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [GDP- forming] subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 O19069
- Every structure of UniProt P53590
- Elsewhere: RCSB PDB 5CAE · PDBe 5CAE · UniProt O19069 · UniProt P53590
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