Research workbench
Structure of succinyl-CoA: 3-ketoacid CoA transferase from drosophila melanogaster
Analyse Structure of succinyl-CoA: 3-ketoacid CoA transferase from drosophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KGB
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:3-ketoacid-coenzyme a transferase
- EC
- 2.8.3.5
- UniProt
- Q9W058
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:3-ketoacid-coenzyme a transferase (EC 2.8.3.5) | protein | 466 | 22% helix, 31% strand | Q9W058 |
| B | Succinyl-COA:3-ketoacid-coenzyme a transferase (EC 2.8.3.5) | protein | 464 | 22% helix, 31% strand | Q9W058 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.84 | 0.94 | 45 | empty |
| 2 | 537 | 0.70 | 0.80 | 82 | empty |
| 3 | 425 | 0.67 | 0.80 | 62 | empty |
| 4 | 220 | 0.62 | 0.81 | 38 | empty |
| 5 | 377 | 0.60 | 0.76 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 2229 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4KGB · Structure of succinyl-CoA: 3-ketoacid CoA transferase from Drosophila melanogaster · the same entry in another collection · chain A against A, TM-score 1.00
- Q9W058 · AlphaFold monomer V2.0 prediction for succinyl-COA:3-ketoacid- coenzyme a transferase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9W058
- Elsewhere: RCSB PDB 4KGB · PDBe 4KGB · UniProt Q9W058
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