MolNFT v1 · #90952 · protein

Free KDM6B structure

4EZ4 · Lysine-specific demethylase 6B: “Free KDM6B structure”. X-ray diffraction, 3 ligands (OGA, NI, ZN), 12 pockets (best druggability 0.79). MolNFT v1 #90952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4EZ4
Type: protein
Length: 895 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 6B
EC: 1.14.112.-
UniProt: Q5NCY0
Ligands: OGA, NI, ZN
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 6B (EC 1.14.112.-)	protein	448	35% helix, 23% strand	Q5NCY0
B	Lysine-specific demethylase 6B (EC 1.14.112.-)	protein	447	34% helix, 23% strand	Q5NCY0

Ligands and binding sites

OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 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

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.79	0.80	113	empty
2	407	0.66	0.79	43	OGA
3	322	0.66	0.81	39	OGA, NI
4	269	0.58	0.78	24	empty
5	114	0.57	0.84	19	empty

Interfaces

1 interface between chains.

A–B · 1149 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4EZ4 · free KDM6B structure · the same entry in another collection · chain A against A, TM-score 1.00
Q5NCY0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6B (Q5NCY0) · a predicted model of the same protein · chain B 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 Q5NCY0
Elsewhere: RCSB PDB 4EZ4 · PDBe 4EZ4 · UniProt Q5NCY0

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