MolNFT v1 · #135250 · protein

Crystal structure of catalytic domain of glp with MS012

5TTG · Histone-lysine N-methyltransferase EHMT1: “Crystal structure of catalytic domain of glp with MS012”. X-ray diffraction, 5 ligands (SAM, 7KZ, ZN), 8 pockets (best druggability 0.78). MolNFT v1 #135250 on GenesisL1: 3D structure…

PDB: 5TTG
Type: protein
Length: 518 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase EHMT1
EC: 2.1.1.-, 2.1.1.43
UniProt: Q9H9B1
Ligands: SAM, 7KZ, ZN, UNX, CL
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43)	protein	260	10% helix, 26% strand	Q9H9B1
B	Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43)	protein	258	10% helix, 26% strand	Q9H9B1

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
7KZ · N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 8 copies · chains A, B
UNX · Unknown atom or ion · ion · 15 copies · chains A, B
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · chains A
DMS · Dimethyl sulfoxide · additive · chains 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	1195	0.78	0.80	91	GOL, UNX
2	447	0.65	0.78	54	SAM, 7KZ, UNX
3	275	0.57	0.77	42	7KZ, UNX
4	214	0.55	0.78	23	SAM
5	73	0.42	0.80	18	UNX

Interfaces

1 interface between chains.

A–B · 1070 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5TTG · Crystal structure of catalytic domain of GLP with MS012 · the same entry in another collection · chain A against A, TM-score 1.00
Q9H9B1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT1 (Q9H9B1) · 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 Q9H9B1
Elsewhere: RCSB PDB 5TTG · PDBe 5TTG · UniProt Q9H9B1

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