Research workbench
GTP-specific succinyl-CoA synthetase complexed with mg-GDP in space group P32
Analyse GTP-specific succinyl-CoA synthetase complexed with mg-GDP in space group P32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JMK
- Type
- protein
- Length
- 1,327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial; Succinate--CoA…
- EC
- 6.2.1.4, 6.2.1.5
- UniProt
- O19069, P53590
- Ligands
- GDP, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% 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 | 297 | 38% helix, 21% strand | O19069 |
| B | Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 379 | 36% helix, 24% strand | P53590 |
| C | Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial (EC 6.2.1.4, 6.2.1.5) | protein | 297 | 37% helix, 22% strand | O19069 |
| D | Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 354 | 36% helix, 21% strand | P53590 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.82 | 0.87 | 64 | empty |
| 2 | 753 | 0.74 | 0.80 | 95 | empty |
| 3 | 1046 | 0.72 | 0.76 | 114 | empty |
| 4 | 206 | 0.57 | 0.79 | 24 | GDP, MG |
| 5 | 233 | 0.54 | 0.77 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2473 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2060 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 553 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 7JMK · GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32 · the same entry in another collection · chain D against D, 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 C 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 0.95
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 7JMK · PDBe 7JMK · UniProt O19069 · UniProt P53590
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