MolNFT v1 · #75116 · protein
Crystal structure of the carboxyltransferase domain of S. cerevisiae acetyl CoA carboxylase in complex with pinoxaden
3PGQ · Acetyl-CoA carboxylase: “Crystal structure of the carboxyltransferase domain of S. cerevisiae acetyl CoA carboxylase in complex with…”. X-ray diffraction, 1 ligand (GY3), 20 pockets (best druggability 0.81). MolNFT v1 #75116 on…
- PDB
- 3PGQ
- Type
- protein
- Length
- 2,043 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA carboxylase
- EC
- 6.4.1.2
- UniProt
- D6W1J1
- Ligands
- GY3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA carboxylase (EC 6.4.1.2) | protein | 688 | 40% helix, 20% strand | D6W1J1 |
| B | Acetyl-CoA carboxylase (EC 6.4.1.2) | protein | 680 | 37% helix, 20% strand | D6W1J1 |
| C | Acetyl-CoA carboxylase (EC 6.4.1.2) | protein | 675 | 38% helix, 20% strand | D6W1J1 |
Ligands and binding sites
- GY3 · 8-(2-ethenyl-6-ethyl-4-methylphenyl)tetrahydro-7H-pyrazolo[1,2-d][1,4,5]oxadiazepine-7,9(8H)-dione · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.81 | 0.84 | 61 | empty |
| 2 | 501 | 0.76 | 0.84 | 33 | empty |
| 3 | 459 | 0.75 | 0.84 | 57 | GY3 |
| 4 | 410 | 0.73 | 0.83 | 46 | GY3 |
| 5 | 497 | 0.72 | 0.82 | 31 | empty |
Interfaces
2 interfaces between chains.
- B–C · 5733 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1350 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3PGQ · Crystal Structure of the Carboxyltransferase Domain of S. cerevisiae Acetyl 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 D6W1J1
- Elsewhere: RCSB PDB 3PGQ · PDBe 3PGQ · UniProt D6W1J1
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