MolNFT v1 · #116437 · protein
Succinyl-COA:ACETATE CoA-transferase (AARCH6-N347A) in complex with CoA
5DDK · Acetyl-CoA hydrolase: “Succinyl-COA:ACETATE CoA-transferase (AARCH6-N347A) in complex with CoA”. X-ray diffraction, 2 ligands (COA, CL), 11 pockets (best druggability 0.79). MolNFT v1 #116437 on GenesisL1: 3D structure, binding…
- PDB
- 5DDK
- Type
- protein
- Length
- 1,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA hydrolase
- EC
- 2.8.3.18
- UniProt
- A0A063X8M7
- Ligands
- COA, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA hydrolase (EC 2.8.3.18) | protein | 512 | 34% helix, 21% strand | A0A063X8M7 |
| B | Acetyl-CoA hydrolase (EC 2.8.3.18) | protein | 504 | 35% helix, 21% strand | A0A063X8M7 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.79 | 0.96 | 38 | CL |
| 2 | 67 | 0.73 | 0.97 | 23 | IMD |
| 3 | 575 | 0.72 | 0.80 | 76 | COA |
| 4 | 496 | 0.71 | 0.80 | 72 | COA |
| 5 | 83 | 0.62 | 0.89 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3596 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5DDK · Succinyl-CoA:acetate CoA-transferase (AarCH6-N347A) in complex with CoA · 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 5DDK · PDBe 5DDK · UniProt A0A063X8M7
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