Research workbench
E. COLI beta-hydroxydecanoyl thiol ester dehydrase modified by its classic mechanism-based inactivator, 3-decynoyl-N- acetyl cysteamine
Analyse E. COLI beta-hydroxydecanoyl thiol ester dehydrase modified by its classic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MKA
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hydroxydecanoyl thiol ester dehydrase
- EC
- 4.2.1.60
- UniProt
- P0A6Q3
- Ligands
- DAC
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-hydroxydecanoyl thiol ester dehydrase (EC 4.2.1.60) | protein | 171 | 18% helix, 36% strand | P0A6Q3 |
Ligands and binding sites
- DAC · 2-decenoyl N-acetyl cysteamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.97 | 32 | DAC |
| 2 | 126 | 0.78 | 0.96 | 32 | DAC |
| 3 | 57 | 0.35 | 0.78 | 14 | empty |
| 4 | 65 | 0.34 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1656 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1MKA · E. COLI beta-hydroxydecanoyl thiol ester dehydrase modified by its classic… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6Q3 · AlphaFold monomer V2.0 prediction for 3-hydroxydecanoyl-[acyl- carrier-protein]… · a predicted model of the same protein · chain B 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 P0A6Q3
- Elsewhere: RCSB PDB 1MKA · PDBe 1MKA · UniProt P0A6Q3
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