Structure of PDB 6kda Chain D

Receptor sequence
>6kdaD (length=284) Species: 9606 (Homo sapiens) [Search protein sequence]
MRRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHE
GNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTG
RLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPV
MIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLK
KVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVS
NMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
3D structure
PDB6kda Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
ChainD
Resolution2.909 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 D S649 C651 N652 S655 V657 E697 V699 R733 Q772 T773 T776 K777 K785 R832 S80 C82 N83 S86 V88 E128 V130 R164 Q203 T204 T207 K208 K216 R263
BS02 dna D N656 V657 P659 M702 K703 N87 V88 P90 M133 K134
BS03 SAH D F581 G583 T586 E605 V606 D627 V628 R832 S833 W834 F12 G14 T17 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
PDBsum6kda
PubMed32083663
UniProtQ9UBC3|DNM3B_HUMAN DNA (cytosine-5)-methyltransferase 3B (Gene Name=DNMT3B)

[Back to BioLiP]