MolNFT v1 · #119606 · protein
Bordetella alcaligenes hdah bound to pfsaha
5G1A · Histone deacetylase-like amidohydrolase: “Bordetella alcaligenes hdah bound to pfsaha”. X-ray diffraction, 3 ligands (7H1, K, ZN), 8 pockets (best druggability 0.65). MolNFT v1 #119606 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5G1A
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase-like amidohydrolase
- EC
- 3.5.1.4
- UniProt
- Q70I53
- Ligands
- 7H1, K, ZN
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase-like amidohydrolase (EC 3.5.1.4) | protein | 369 | 39% helix, 14% strand | Q70I53 |
| B | Histone deacetylase-like amidohydrolase (EC 3.5.1.4) | protein | 371 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- 7H1 · 2,2,3,3,4,4,5,5,6,6,7,7-dodecakis(fluoranyl)-~{N}-oxidanyl-~{N}'-phenyl-octanediamide · ligand · 2 copies · 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 · 8 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.65 | 0.84 | 39 | empty |
| 2 | 182 | 0.64 | 0.85 | 40 | empty |
| 3 | 436 | 0.64 | 0.77 | 39 | empty |
| 4 | 374 | 0.57 | 0.75 | 47 | empty |
| 5 | 93 | 0.50 | 0.82 | 23 | 7H1 |
Interfaces
1 interface between chains.
- A–B · 397 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 5G1A · PDBe 5G1A · UniProt Q70I53
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.