Structure of PDB 6kda Chain A

Receptor sequence

>6kdaA (length=284) Species: 9606 (Homo sapiens) [Search protein sequence]

MRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHE
GNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTG
RLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPV
MIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLK
KVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVS
NMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE

3D structure

PDB

6kda Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.

Chain

Resolution

2.909 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.1.1.37: DNA (cytosine-5-)-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	N656 V657 P659 M702 K703 V704 G824	N87 V88 P90 M133 K134 V135 G255
BS02	dna	A	S649 C651 N652 S655 V657 R733 Q772 T773 T776 K777 K785 G831 R832	S80 C82 N83 S86 V88 R164 Q203 T204 T207 K208 K216 G262 R263
BS03	SAH	A	F581 D582 G583 T586 S604 E605 V606 D627 V628 R832 S833 W834	F12 D13 G14 T17 S35 E36 V37 D58 V59 R263 S264 W265	BindingDB: IC50=300nM

Gene Ontology

	Molecular Function
GO:0008168	methyltransferase activity

View graph for
Molecular Function

External links

PDB	RCSB:6kda, PDBe:6kda, PDBj:6kda
PDBsum	6kda
PubMed	32083663
UniProt	Q9UBC3\|DNM3B_HUMAN DNA (cytosine-5)-methyltransferase 3B (Gene Name=DNMT3B)

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