Research workbench
Crystal structure of peroxisomal KAT2 from arabidopsis thaliana
Analyse Crystal structure of peroxisomal KAT2 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WU9
- Type
- protein
- Length
- 805 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketoacyl-CoA thiolase 2, peroxisomal
- EC
- 2.3.1.16
- UniProt
- Q56WD9
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-ketoacyl-CoA thiolase 2, peroxisomal (EC 2.3.1.16) | protein | 403 | 43% helix, 22% strand | Q56WD9 |
| B | 3-ketoacyl-CoA thiolase 2, peroxisomal (EC 2.3.1.16) | protein | 402 | 41% helix, 23% strand | Q56WD9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.69 | 0.80 | 60 | empty |
| 2 | 422 | 0.67 | 0.79 | 58 | EDO |
| 3 | 203 | 0.56 | 0.79 | 59 | EDO |
| 4 | 168 | 0.44 | 0.74 | 23 | empty |
| 5 | 117 | 0.42 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2621 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 2WU9 · Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q56WD9 · AlphaFold monomer V2.0 prediction for 3-ketoacyl-CoA thiolase 2, peroxisomal (Q56WD9) · a predicted model of the same protein · chain B 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 Q56WD9
- Elsewhere: RCSB PDB 2WU9 · PDBe 2WU9 · UniProt Q56WD9
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