Structure of PDB 7xi9 Chain A

Receptor sequence

>7xi9A (length=869) Species: 9606 (Homo sapiens)

GPTKATTTKLVYQIFDTFFAEQIEKDRCGVCEVCQQPECGKCKACKDMVK
FGGSGRSKQACQERRCPNMAMTLEVGDCVSVIPDDSSKPLYLARVTALWE
DSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKV
IYKAPSENWAMEGGMGKTYFYQLWYDQDYARFESPPKTQPKFCVSCARLA
EMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNI
KLPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPN
ETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRC
TVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSLPKLR
TLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTED
CNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTY
SKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRM
GYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQ
LSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNG
EPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLP
NIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAAR
QFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVL
HPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGL
EIKLCMLAKARESASAKIK

3D structure

• PDB: 7xi9 Structural basis for activation of DNMT1.
• Chain: A
• Resolution: 2.52 Å

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	G1231 N1233 R1234 R1269 R1490 C1499 H1502 T1503 R1506 H1507 W1510 K1535	G491 N493 R494 R529 R750 C759 H762 T763 R766 H767 W770 K795
BS02	dna	A	S977 Y979 K981 P1224 P1225 C1226 Q1227 S1230 M1232 N1233 F1235 R1238 Y1240 E1266 V1268 R1312 N1508 T1528 G1534 K1535 N1578	S267 Y269 K271 P484 P485 C486 Q487 S490 M492 N493 F495 R498 Y500 E526 V528 R572 N768 T788 G794 K795 N838
BS03	ZN	A	C1476 C1478 C1485 H1502	C736 C738 C745 H762
BS04	ZN	A	H793 C820 C893 C896	H109 C136 C193 C196
BS05	ZN	A	C656 C659 C691	C31 C34 C66
BS06	ZN	A	C664 C670 C686	C39 C45 C61
BS07	SAH	A	F1145 S1146 L1151 E1168 M1169 W1170 D1190 L1247 N1578 A1579 V1580	F405 S406 L411 E428 M429 W430 D450 L507 N838 A839 V840

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:7xi9, PDBe:7xi9, PDBj:7xi9
• PDBsum: 7xi9
• PubMed: 36414620
• UniProt: P26358|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)