Research workbench
Structure of hdac like protein from bordetella alcaligenes in complex with the photoswitchable inhibitor CEW65
Analyse Structure of hdac like protein from bordetella alcaligenes in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G3W
- Type
- protein
- Length
- 1,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase-like amidohydrolase
- UniProt
- Q70I53
- Ligands
- C65, K, ZN
- Pockets
- 12 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Histone deacetylase-like amidohydrolase | protein | 369 | 40% helix, 14% strand | Q70I53 |
| D | Histone deacetylase-like amidohydrolase | protein | 371 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- C65 · (2E)-N-hydroxy-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-enamide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.90 | 0.93 | 107 | empty |
| 2 | 629 | 0.82 | 0.87 | 93 | empty |
| 3 | 512 | 0.78 | 0.85 | 68 | empty |
| 4 | 65 | 0.72 | 0.97 | 31 | empty |
| 5 | 504 | 0.66 | 0.77 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1772 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1766 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 943 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5G3W · Structure of HDAC like protein from Bordetella Alcaligenes in complex with the… · 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 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 Q70I53
- Elsewhere: RCSB PDB 5G3W · PDBe 5G3W · UniProt Q70I53
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