Research workbench
Succinyl-COA:ACETATE CoA-transferase (AARCH6) bound to acetate
Analyse Succinyl-COA:ACETATE CoA-transferase (AARCH6) bound to acetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DW4
- Type
- protein
- Length
- 1,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:ACETATE CoA-transferase
- UniProt
- A0A063X8M7
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:ACETATE CoA-transferase | protein | 512 | 35% helix, 20% strand | A0A063X8M7 |
| B | Succinyl-COA:ACETATE CoA-transferase | protein | 504 | 34% helix, 21% strand | A0A063X8M7 |
Ligands and binding sites
- ACT · Acetate ion · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.83 | 0.97 | 49 | ACT |
| 2 | 666 | 0.76 | 0.82 | 75 | IMD, ACT |
| 3 | 75 | 0.73 | 0.97 | 26 | IMD |
| 4 | 691 | 0.73 | 0.79 | 81 | ACT |
| 5 | 90 | 0.63 | 0.89 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3546 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5DW4 · Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A063X8M7
- Elsewhere: RCSB PDB 5DW4 · PDBe 5DW4 · UniProt A0A063X8M7
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