MolNFT v1 · #169948 · protein
GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme a, magnesium ions and succinates
6XRU · Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha…: “GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme a, magnesium ions and succinates”. X-ray diffraction, 3 ligands (DCA, MG, PO4), 5 pockets (best druggability…
- PDB
- 6XRU
- Type
- protein
- Length
- 702 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; Succinate--CoA ligase…
- EC
- 6.2.1.4, 6.2.1.5
- UniProt
- O19069, P53590
- Ligands
- DCA, MG, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% 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 | 309 | 37% helix, 22% strand | O19069 |
| B | Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 393 | 38% helix, 24% strand | P53590 |
Ligands and binding sites
- DCA · Desulfo-coenzyme A · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.81 | 0.82 | 101 | DCA, SIN, PO4, GOL, MG |
| 2 | 176 | 0.60 | 0.83 | 29 | empty |
| 3 | 147 | 0.47 | 0.77 | 18 | empty |
| 4 | 97 | 0.37 | 0.75 | 25 | empty |
| 5 | 79 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2256 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6XRU · GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions… · 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 0.98
- 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 0.90
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 6XRU · PDBe 6XRU · UniProt O19069 · UniProt P53590
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