Research workbench
Crystal structure of the carboxyltransferase domain of S. cerevisiae acetyl CoA carboxylase in complex with pinoxaden
Analyse Crystal structure of the carboxyltransferase domain of S. cerevisiae acetyl CoA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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