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A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase
Analyse A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GJK
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.47
- Source
- Alcaligenaceae bacterium FB188
- Molecule
- Histone deacetylase-like amidohydrolase
- EC
- 3.5.1.-
- UniProt
- Q70I53
- Ligands
- F0Z, MLT, K, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.47 · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 369 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- F0Z · 2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol · ligand · 4 copies · chains A, B
- MLT · D-malate · ligand · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.67 | 0.77 | 66 | empty |
| 2 | 434 | 0.63 | 0.77 | 41 | F0Z, MLT, PEG |
| 3 | 50 | 0.48 | 0.85 | 17 | ACT |
Interfaces
1 interface between chains.
- A–B · 386 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6GJK · A degradation product of pd 404182 (P2742) bound to histone deacetylase-like… · the same entry in another collection · chain A against A, TM-score 1.00
- Q70I53 · AlphaFold monomer V2.0 prediction for histone deacetylase-like amidohydrolase (Q70I53) · 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 Q70I53
- Elsewhere: RCSB PDB 6GJK · PDBe 6GJK · UniProt Q70I53
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