Research workbench
Crystal structure of a hdac-like protein hdah from bordetella sp. with the bound inhibitor st-17
Analyse Crystal structure of a hdac-like protein hdah from bordetella sp. with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VCG
- Type
- protein
- Length
- 1,479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase-like amidohydrolase
- EC
- 3.5.1.-
- UniProt
- Q70I53
- Ligands
- S17, K, ZN, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 368 | 40% helix, 14% strand | Q70I53 |
| B, C | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 368 | 39% helix, 14% strand | Q70I53 |
| D | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 375 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- S17 · methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate · ligand · 4 copies · chains A, D, B, C
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.78 | 0.92 | 36 | empty |
| 2 | 226 | 0.77 | 0.91 | 36 | empty |
| 3 | 131 | 0.65 | 0.88 | 35 | empty |
| 4 | 125 | 0.64 | 0.87 | 35 | empty |
| 5 | 126 | 0.62 | 0.87 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1773 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1767 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2VCG · Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound… · the same entry in another collection · chain D against D, 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 2VCG · PDBe 2VCG · UniProt Q70I53
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.