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The 1.8 ångström crystal structure of the dimeric peroxisomal thiolase of saccharomyces cerevisiae
Analyse The 1.8 ångström crystal structure of the dimeric peroxisomal thiolase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AFW
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketoacetyl-CoA thiolase
- EC
- 2.3.1.16
- UniProt
- P27796
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-ketoacetyl-CoA thiolase (EC 2.3.1.16) | protein | 390 | 42% helix, 21% strand | P27796 |
| B | 3-ketoacetyl-CoA thiolase (EC 2.3.1.16) | protein | 393 | 41% helix, 20% strand | P27796 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.72 | 0.81 | 50 | MRD |
| 2 | 534 | 0.71 | 0.80 | 48 | MRD |
| 3 | 65 | 0.36 | 0.78 | 16 | empty |
| 4 | 67 | 0.36 | 0.77 | 11 | empty |
| 5 | 71 | 0.34 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2499 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1AFW · The 1.8 ångström crystal structure of the dimeric peroxisomal thiolase of saccharomyces… · the same entry in another collection · chain A against A, TM-score 1.00
- P27796 · AlphaFold monomer V2.0 prediction for 3-ketoacyl-CoA thiolase, peroxisomal (P27796) · a predicted model of the same protein · 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 P27796
- Elsewhere: RCSB PDB 1AFW · PDBe 1AFW · UniProt P27796
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