Structure of PDB 4wxx Chain B

Receptor sequence

>4wxxB (length=1178) Species: 9606 (Homo sapiens)

PKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIEALPQHKLTCFS
VYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPI
NEWWITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKI
VVEFLQSNSDSTYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQV
ESYDEAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARRQPTKATTTKL
VYQIFDTFFAEQIEKKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSK
QACQERRCPNMAMKEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISW
VGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALW
EDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVK
VIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQ
PTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILY
RVGDGVYLPPEAFTFNIKRKEPVDEDLYPEHYRKYSLDAPEPYRIGRIKE
IFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEE
AVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFED
PPNHARSKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAF
RLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQ
GFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRS
MVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLF
PEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEV
RNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRH
IPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCS
CVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTV
TNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVG
NAVPPPLAKAIGLEIKLCMLAKALTRVW

3D structure

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

Enzymatic activity

• Catalytic site (original residue number in PDB): C1226 E1266 R1310 R1312
• Catalytic site (residue number reindexed from 1): C799 E839 R883 R885
• 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	B	C1476 C1478 C1485 H1502	C1049 C1051 C1058 H1075
BS02	ZN	B	H793 C820 C893 C896	H410 C437 C510 C513
BS03	ZN	B	C670 C686	C287 C303
BS04	ZN	B	C653 C656 C659 C691	C270 C273 C276 C308
BS05	ZN	B	C353 C356 C414 H418	C3 C6 C53 H57
BS06	SAH	B	F1145 G1147 G1150 L1151 E1168 M1169 D1190 C1191 N1578 A1579 V1580	F718 G720 G723 L724 E741 M742 D763 C764 N1151 A1152 V1153

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)