Structure of PDB 4wxx Chain A

Receptor sequence

>4wxxA (length=1169) Species: 9606 (Homo sapiens)

PKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKALPQHKLTCFSVYCK
HGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWW
ITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEF
LQSNSDSTYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYD
EAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARRQTKATTTKLVYQIF
DTFFAEQIEKKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQE
RRCPNMAMKEADDDEEVDDNIPEMPSPKKMQGKKKKQNKNRISWVGEAVK
TDKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQ
MFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPS
ENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKF
KFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVY
LPPEAFTFNIRKEPVDEDLYPEHYRKYLDAPEPYRIGRIKEIFCPKKSNG
RPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQ
GRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSKL
PKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTV
FTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFN
SRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRC
LVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAP
RACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEI
SYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDW
RDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACD
PAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQ
GRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAK
AIGLEIKLCMLAKALTRVW

3D structure

• PDB: 4wxx Crystal Structure of Human DNA Methyltransferase 1.
• Chain: A
• Resolution: 2.622 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C1226 E1266 R1310 R1312
• Catalytic site (residue number reindexed from 1): C790 E830 R874 R876
• 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	ZN	A	C1476 C1478 C1485 H1502	C1040 C1042 C1049 H1066
BS02	ZN	A	H793 C820 C893 C896	H403 C430 C503 C506
BS03	ZN	A	C670 C686	C282 C298
BS04	ZN	A	C653 C656 C659 C691	C265 C268 C271 C303
BS05	ZN	A	C353 C356 H418	C3 C6 H53
BS06	SAH	A	F1145 S1146 G1147 G1150 L1151 E1168 M1169 D1190 C1191 L1247 N1578 V1580	F709 S710 G711 G714 L715 E732 M733 D754 C755 L811 N1142 V1144

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003886 DNA (cytosine-5-)-methyltransferase activity
• GO:0008168 methyltransferase activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0006346 DNA methylation-dependent heterochromatin formation

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:4wxx, PDBe:4wxx, PDBj:4wxx
• PDBsum: 4wxx
• PubMed: 26070743
• UniProt: P26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)