MolNFT v1 · #30286 · protein
Crystal structure of a hdac-like protein with cypx bound
1ZZ3 · Histone deacetylase-like amidohydrolase: “Crystal structure of a hdac-like protein with cypx bound”. X-ray diffraction, 3 ligands (3YP, K, ZN), 9 pockets (best druggability 0.78). MolNFT v1 #30286 on GenesisL1: 3D structure, binding…
- PDB
- 1ZZ3
- Type
- protein
- Length
- 1,468 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
- 3YP, K, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Histone deacetylase-like amidohydrolase (EC 3.5.1.-) | protein | 367 | 40% helix, 15% strand | Q70I53 |
Ligands and binding sites
- 3YP · 3-cyclopentyl-N-hydroxypropanamide · ligand · 4 copies · chains A, D, B, C
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.78 | 0.91 | 35 | empty |
| 2 | 256 | 0.77 | 0.90 | 36 | empty |
| 3 | 104 | 0.69 | 0.92 | 38 | empty |
| 4 | 51 | 0.69 | 0.97 | 25 | empty |
| 5 | 99 | 0.65 | 0.90 | 37 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1802 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1800 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1ZZ3 · Crystal structure of a HDAC-like protein with CypX bound · 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 1ZZ3 · PDBe 1ZZ3 · UniProt Q70I53
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