Research workbench
Crystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene glycol
Analyse Crystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FPI
- 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
- SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% 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 | 35% helix, 21% strand | — |
| B | Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial (EC 6.2.1.4) | protein | 393 | 37% helix, 24% strand | P53590 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.75 | 0.81 | 60 | SO4 |
| 2 | 294 | 0.67 | 0.83 | 40 | empty |
| 3 | 167 | 0.62 | 0.84 | 28 | SO4 |
| 4 | 161 | 0.57 | 0.82 | 28 | empty |
| 5 | 66 | 0.51 | 0.85 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2154 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2FPI · Crystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene glycol · the same entry in another collection · 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 0.94
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 2FPI · PDBe 2FPI · UniProt P53590
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