Research workbench
Crystal structure of hdac-like protein from P. aeruginosa in complex with a photo-switchable inhibitor.
Analyse Crystal structure of hdac-like protein from P. aeruginosa in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LI3
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoin utilization protein
- UniProt
- A0A0D6GAJ7
- Ligands
- 9RB, K, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetoin utilization protein | protein | 374 | 42% helix, 17% strand | A0A0D6GAJ7 |
| B | Acetoin utilization protein | protein | 368 | 42% helix, 17% strand | A0A0D6GAJ7 |
Ligands and binding sites
- 9RB · (2E)-N-hydroxy-3-{4-[(E)-(1,3,5-trimethyl-1H-pyrazol-4-yl)diazenyl]phenyl}prop-2-enamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.79 | 0.88 | 57 | empty |
| 2 | 193 | 0.68 | 0.86 | 38 | 9RB |
| 3 | 146 | 0.65 | 0.87 | 32 | 9RB |
Interfaces
1 interface between chains.
- A–B · 2118 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5LI3 · Crystal structure of HDAC-like protein from P. aeruginosa in complex with a… · the same entry in another collection · chain B against B, 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 A0A0D6GAJ7
- Elsewhere: RCSB PDB 5LI3 · PDBe 5LI3 · UniProt A0A0D6GAJ7
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