Research workbench
Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP
Analyse Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FPG
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial; Succinyl-CoA ligase…
- EC
- 6.2.1.4
- UniProt
- P53590
- Ligands
- GDP, K, PO4
- Pockets
- 4 · 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 [GDP-forming] alpha-chain, mitochondrial (EC 6.2.1.4) | protein | 305 | 37% helix, 22% strand | — |
| B | Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial (EC 6.2.1.4) | protein | 393 | 39% helix, 23% strand | P53590 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.81 | 0.82 | 115 | K, GDP |
| 2 | 309 | 0.72 | 0.85 | 40 | PO4 |
| 3 | 170 | 0.57 | 0.81 | 27 | empty |
| 4 | 58 | 0.34 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2157 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2FPG · Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP · the same entry in another collection · chain B against B, 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 0.95
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 P53590
- Elsewhere: RCSB PDB 2FPG · PDBe 2FPG · UniProt P53590
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