MolNFT v1 · #117033 · protein
Succinyl-COA:ACETATE CoA-transferase (AARCH6) bound to the CoA analogue 3'-phosphoadenosine 5'-(O-(N-propylpantothenamide)) pyrophosphate (mx)
5DW5: “Succinyl-COA:ACETATE CoA-transferase (AARCH6) bound to the CoA analogue 3'-phosphoadenosine…”. X-ray diffraction, 2 ligands (0T1, CL), 11 pockets (best druggability 0.83). MolNFT v1 #117033 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DW5
- Type
- protein
- Length
- 1,015 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:ACETATE CoA-transferase
- EC
- 2.8.3.18
- UniProt
- A0A063X8M7
- Ligands
- 0T1, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:ACETATE CoA-transferase (EC 2.8.3.18) | protein | 512 | 34% helix, 21% strand | A0A063X8M7 |
| B | Succinyl-COA:ACETATE CoA-transferase (EC 2.8.3.18) | protein | 503 | 36% helix, 21% strand | A0A063X8M7 |
Ligands and binding sites
- 0T1 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(propylamino)propyl]amino]butyl] hydrogen phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.83 | 0.96 | 51 | CL |
| 2 | 632 | 0.74 | 0.80 | 71 | 0T1 |
| 3 | 67 | 0.72 | 0.97 | 24 | IMD |
| 4 | 507 | 0.69 | 0.79 | 62 | 0T1 |
| 5 | 68 | 0.67 | 0.94 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3532 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 5DW5 · Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to the CoA analogue… · 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 5DW5 · PDBe 5DW5 · UniProt A0A063X8M7
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