PDBsum entry 7x9d

Transferase

PDB id: 7x9d

Contents

Protein chains

277 a.a.

191 a.a.

Ligands

HRM ×2

PDB id:

7x9d

Name:

Transferase

Title:

Dnmt3b in complex with harmine

Structure:

DNA (cytosine-5)-methyltransferase 3b. Chain: a, d. Synonym: dnmt3b,DNA methyltransferase hsaiiib,m.Hsaiiib. Engineered: yes. DNA (cytosine-5)-methyltransferase 3-like. Chain: b, c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dnmt3b. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: dnmt3l. Expression_system_taxid: 562

Resolution:

3.08Å R-factor: 0.215 R-free: 0.245

Authors:

C.-C.Cho,H.S.Yuan

Key ref:

C.-C.Cho and h.s.yuan Structural insights into inhibition of human DNA methyltransferases by harmine. To be published, . PubMed id: 37188336

Date:

15-Mar-22 Release date: 15-Mar-23

Protein chains

Q9UBC3  (DNM3B_HUMAN) -  DNA (cytosine-5)-methyltransferase 3B from Homo sapiens

Seq: 853 a.a.

Struc: 277 a.a.*

Protein chains

Q9UJW3  (DNM3L_HUMAN) -  DNA (cytosine-5)-methyltransferase 3-like from Homo sapiens

Seq: 386 a.a.

Struc: 191 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, D: E.C.2.1.1.37 - Dna (cytosine-5-)-methyltransferase.
• Reaction: a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl- 2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H⁺

2'-deoxycytidine in DNA + S-adenosyl-L-methionine = 5-methyl- 2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = HRM) matches with 40.00% similarity)

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