PDBsum entry 7o2b

Transferase

PDB id: 7o2b

Contents

Protein chain

427 a.a.

Ligands

UZQ

SAM

Metals

_ZN ×3

Waters ×203

PDB id:

7o2b

Name:

Transferase

Title:

X-ray structure of smyd3 in complex with benzodiazepine-type inhibitor 6

Structure:

Histone-lysine n-methyltransferase smyd3. Chain: a. Synonym: set and mynd domain-containing protein 3,zinc finger mynd domain-containing protein 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: smyd3, zmynd1, znfn3a1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.03Å R-factor: 0.204 R-free: 0.258

Authors:

H.Steuber

Key ref:

S.Gradl et al. (2021). Discovery of the smyd3 inhibitor bay-6035 using therm shift assay (tsa)-Based high-Throughput screening.. Slas discov, 26, 947. PubMed id: 34154424

Date:

30-Mar-21 Release date: 07-Jul-21

Protein chain

Q9H7B4  (SMYD3_HUMAN) -  Histone-lysine N-methyltransferase SMYD3 from Homo sapiens

Seq: 428 a.a.

Struc: 427 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.354 - [histone H3]-lysine(4) N-trimethyltransferase.
• Reaction: L-lysyl₄-[histone H3] + 3 S-adenosyl-L-methionine = N₆,N₆,N₆- trimethyl-L-lysyl₄-[histone H3] + 3 S-adenosyl-L-homocysteine + 3 H⁺

L-lysyl(4)-[histone H3] + 3 × S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = N(6),N(6),N(6)- trimethyl-L-lysyl(4)-[histone H3] + 3 × S-adenosyl-L-homocysteine + 3 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site