Research workbench
Humanized yeast acc carboxyltransferase domain bound to tert-butyl 7- [(7-methyl-1H-indazol-5-YL)CARBONYL]-2,7-DIAZASPIRO[3.5]NONANE-2- carboxylate
Analyse Humanized yeast acc carboxyltransferase domain bound to tert-butyl 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CTC
- Type
- protein
- Length
- 2,059 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
- 57K, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% 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 | 691 | 40% helix, 22% strand | Q00955 |
| B | Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14) | protein | 687 | 41% helix, 21% strand | Q00955 |
| C | Acetyl-CoA carboxylase (EC 6.4.1.2, 6.3.4.14) | protein | 681 | 42% helix, 21% strand | Q00955 |
Ligands and binding sites
- 57K · tert-butyl 7-[(7-methyl-1H-indazol-5-yl)carbonyl]-2,7-diazaspiro[3.5]nonane-2-carboxylate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.83 | 0.87 | 87 | empty |
| 2 | 487 | 0.76 | 0.84 | 33 | empty |
| 3 | 384 | 0.76 | 0.86 | 45 | 57K |
| 4 | 346 | 0.75 | 0.86 | 49 | 57K |
| 5 | 500 | 0.70 | 0.80 | 36 | empty |
Interfaces
2 interfaces between chains.
- B–C · 5978 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5CTC · Humanized yeast ACC carboxyltransferase domain bound to tert-butyl… · 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 5CTC · PDBe 5CTC · UniProt Q00955
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