Research workbench
Crystal structure of the humanized carboxyltransferase domain of yeast acetyl-CoA caroxylase in complex with compound 1
Analyse Crystal structure of the humanized carboxyltransferase domain of yeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TV5
- Type
- protein
- Length
- 2,070 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA carboxylase
- EC
- 6.4.1.2, 6.3.4.14
- UniProt
- Q00955
- Ligands
- RCP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14) | protein | 696 | 40% helix, 20% strand | Q00955 |
| B | Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14) | protein | 690 | 41% helix, 21% strand | Q00955 |
| C | Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14) | protein | 684 | 41% helix, 21% strand | Q00955 |
Ligands and binding sites
- RCP · (3R)-1'-(9-anthrylcarbonyl)-3-(morpholin-4-ylcarbonyl)-1,4'-bipiperidine · 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 | 1038 | 0.85 | 0.86 | 122 | RCP |
| 2 | 514 | 0.76 | 0.84 | 33 | empty |
| 3 | 288 | 0.72 | 0.85 | 37 | RCP |
| 4 | 534 | 0.71 | 0.80 | 34 | empty |
| 5 | 266 | 0.64 | 0.81 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–C · 5846 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3TV5 · Crystal Structure of the humanized carboxyltransferase domain of yeast Acetyl-coA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00955 · AlphaFold monomer V2.0 prediction for acetyl-CoA carboxylase (Q00955) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q00955
- Elsewhere: RCSB PDB 3TV5 · PDBe 3TV5 · UniProt Q00955
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