MolNFT v1 · #154638 · protein

Crystal structure of HEMK2/TRMT112 in complex with sah and meq

6KHS · Methyltransferase N6AMT1: “Crystal structure of HEMK2/TRMT112 in complex with sah and meq”. X-ray diffraction, 2 ligands (MEQ, SAH), 4 pockets (best druggability 0.76). MolNFT v1 #154638 on GenesisL1: 3D structure, binding sites and…

PDB: 6KHS
Type: protein
Length: 318 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyltransferase N6AMT1; Multifunctional methyltransferase subunit TRM112-like protein
EC: 2.1.1.-, 2.1.1.72
UniProt: Q9Y5N5, Q9UI30
Ligands: MEQ, SAH
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyltransferase N6AMT1 (EC 2.1.1.-, 2.1.1.72)	protein	195	39% helix, 28% strand	Q9Y5N5
B	Multifunctional methyltransferase subunit TRM112-like protein	protein	123	32% helix, 22% strand	Q9UI30

Ligands and binding sites

MEQ · N5-methylglutamine · ligand · chains A
SAH · S-adenosyl-L-homocysteine · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	222	0.76	0.91	44	MEQ, SAH
2	99	0.60	0.87	20	empty
3	169	0.47	0.76	19	empty
4	58	0.30	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 1178 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6KHS · Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5N5 · AlphaFold monomer V2.0 prediction for methyltransferase N6AMT1 (Q9Y5N5) · a predicted model of the same protein · chain A against A, TM-score 0.99
Q9UI30 · AlphaFold monomer V2.0 prediction for multifunctional methyltransferase subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q9Y5N5
Every structure of UniProt Q9UI30
Elsewhere: RCSB PDB 6KHS · PDBe 6KHS · UniProt Q9Y5N5 · UniProt Q9UI30

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