Structure of PDB 5yx2 Chain D

Receptor sequence

>5yx2D (length=285) Species: 9606 (Homo sapiens) [Search protein sequence]

AEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRH
QGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGT
GRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNP
VMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKF
SKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDV
SNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV

3D structure

PDB

5yx2 Structural basis for DNMT3A-mediated de novo DNA methylation.

Chain

Resolution

2.653 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.-
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	S708 C710 N711 S714 V716 P718 E756 V758 R792 R831 T832 T834 T835 R836 G890 R891	S81 C83 N84 S87 V89 P91 E129 V131 R165 R204 T205 T207 T208 R209 G263 R264
BS02	dna	D	V716 P718 V763 S837 N838 S881 R882 L883	V89 P91 V136 S210 N211 S254 R255 L256
BS03	SAH	D	F640 D641 G642 I643 T645 E664 V665 D686 V687 G707 R891 S892 W893	F13 D14 G15 I16 T18 E37 V38 D59 V60 G80 R264 S265 W266	BindingDB: IC50=>50000nM

Gene Ontology

	Molecular Function
GO:0008168	methyltransferase activity

View graph for
Molecular Function

External links

PDB	RCSB:5yx2, PDBe:5yx2, PDBj:5yx2
PDBsum	5yx2
PubMed	29414941
UniProt	Q9Y6K1\|DNM3A_HUMAN DNA (cytosine-5)-methyltransferase 3A (Gene Name=DNMT3A)

[Back to BioLiP]