MolNFT v1 · #178756 · protein
GTP-specific succinyl-CoA synthetase complexed with mg-gmppnp, phosphohistidine loop pointing towards nucleotide binding site
7JKR · Succinate--CoA ligase [ADP/GDP-forming] subunit alpha…: “GTP-specific succinyl-CoA synthetase complexed with mg-gmppnp, phosphohistidine loop pointing towards…”. X-ray diffraction, 2 ligands (GNP, MG), 6 pockets (best druggability…
- PDB
- 7JKR
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial; Succinyl-CoA ligase…
- EC
- 6.2.1.4, 6.2.1.5
- UniProt
- O19069, P53590
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial (EC 6.2.1.4, 6.2.1.5) | protein | 302 | 39% helix, 21% strand | O19069 |
| B | Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 390 | 35% helix, 24% strand | P53590 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.70 | 0.84 | 46 | empty |
| 2 | 174 | 0.66 | 0.86 | 35 | empty |
| 3 | 237 | 0.61 | 0.81 | 34 | GNP, MG |
| 4 | 60 | 0.56 | 0.88 | 16 | empty |
| 5 | 193 | 0.54 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2628 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 7JKR · GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, phosphohistidine loop… · 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 0.96
- 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 0.95
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 7JKR · PDBe 7JKR · UniProt O19069 · UniProt P53590
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