MolNFT v1 · #89950 · protein

Crystal structure of histone demethylase NO66

4E4H · Lysine-specific demethylase NO66: “Crystal structure of histone demethylase NO66”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.74). MolNFT v1 #89950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4E4H
Type: protein
Length: 1,825 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase NO66
EC: 1.14.11.27
UniProt: Q9H6W3
Ligands: FE
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase NO66 (EC 1.14.11.27)	protein	455	38% helix, 22% strand	Q9H6W3
B	Lysine-specific demethylase NO66 (EC 1.14.11.27)	protein	458	38% helix, 22% strand	Q9H6W3
C	Lysine-specific demethylase NO66 (EC 1.14.11.27)	protein	455	38% helix, 21% strand	Q9H6W3
D	Lysine-specific demethylase NO66 (EC 1.14.11.27)	protein	457	38% helix, 22% strand	Q9H6W3

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains A
GOL · Glycerol · additive · chains B, C
PEG · Di(hydroxyethyl)ether · additive · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	708	0.74	0.79	89	empty
2	308	0.73	0.86	50	empty
3	259	0.72	0.86	34	empty
4	283	0.71	0.85	47	empty
5	555	0.71	0.80	72	FE, GOL

Interfaces

4 interfaces between chains.

B–C · 3356 Å² buried · 56 hydrogen bonds · protein-protein
A–D · 3273 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 1269 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1220 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4E4H · Crystal structure of Histone Demethylase NO66 · the same entry in another collection · chain D against D, TM-score 1.00
Q9H6W3 · AlphaFold monomer V2.0 prediction for ribosomal oxygenase 1 (Q9H6W3) · a predicted model of the same protein · chain B 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 Q9H6W3
Elsewhere: RCSB PDB 4E4H · PDBe 4E4H · UniProt Q9H6W3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.