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Human euchromatic histone methyltransferase 2

Analyse Human euchromatic histone methyltransferase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O8J
Type: protein
Length: 1,035 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
EC: 2.1.1.43
UniProt: Q96KQ7
Ligands: SAH, ZN
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43)	protein	254	10% helix, 25% strand	Q96KQ7
B	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43)	protein	271	15% helix, 24% strand	Q96KQ7
C	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43)	protein	262	13% helix, 24% strand	Q96KQ7
D	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43)	protein	248	8% helix, 25% strand	Q96KQ7

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 16 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1094	0.80	0.81	77	empty
2	1115	0.80	0.81	70	empty
3	406	0.64	0.78	44	SAH
4	570	0.63	0.75	72	empty
5	317	0.57	0.76	33	empty

Interfaces

4 interfaces between chains.

A–D · 1206 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1157 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 258 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 147 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2O8J · Human euchromatic histone methyltransferase 2 · the same entry in another collection · chain D against D, TM-score 1.00
Q96KQ7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT2 (Q96KQ7) · a predicted model of the same protein · chain D 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 Q96KQ7
Elsewhere: RCSB PDB 2O8J · PDBe 2O8J · UniProt Q96KQ7

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