MolNFT v1 · #85975 · protein

Crystal structure of JMJD3 with gsk-J1

4ASK · Lysine-specific demethylase 6B: “Crystal structure of JMJD3 with gsk-J1”. X-ray diffraction, 3 ligands (K0I, ZN, CO), 8 pockets (best druggability 0.72). MolNFT v1 #85975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ASK
Type: protein
Length: 851 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 6B
EC: 1.14.11.-
UniProt: O15054
Ligands: K0I, ZN, CO
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 6B (EC 1.14.11.-)	protein	428	36% helix, 25% strand	O15054
B	Lysine-specific demethylase 6B (EC 1.14.11.-)	protein	423	36% helix, 24% strand	O15054

Ligands and binding sites

K0I · 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
CO · Cobalt (II) ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	525	0.72	0.81	46	K0I, CO
2	530	0.70	0.79	45	K0I, CO
3	307	0.55	0.75	37	empty
4	203	0.52	0.77	25	empty
5	178	0.46	0.75	27	empty

Interfaces

1 interface between chains.

A–B · 306 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4ASK · Crystal structure of JMJD3 with gsk-J1 · the same entry in another collection · chain A against A, TM-score 1.00
O15054 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6B (O15054) · a predicted model of the same protein · chain A 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 O15054
Elsewhere: RCSB PDB 4ASK · PDBe 4ASK · UniProt O15054

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