Structure of PDB 4da4 Chain B

Receptor sequence

>4da4B (length=832) Species: 10090 (Mus musculus)

DRISWLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLAR
VTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYI
HSKVKVIYKAPSENWAMEGGGKTYFFQLWYNQEYARFESPPKTQPTEDNK
HKFCLSCIRLAELRQKEMPKVLEQIEEVDGRVYCSSITKNGVVYRLGDSV
YLPPEAFTFNIKVASPVKRPKKDPVNETLYPEHYRKYSDYIKGSNLDAPE
PYRIGRIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDIN
MLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYN
SKTKNFEDPPNHARSPGNIKLPKLRTLDVFSGCGGLSEGFHQAGISETLW
AIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKG
DVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLL
ENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAII
LAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTI
TVRDTMSDLPEIQNGASNSEIPYNGEPLSWFQRQLRGSHYQPILRDHICK
DMSPLVAARMRHIPLFPGSDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNG
YSSTGALRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGR
LEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFF
GNILDRHRQVGNAVPPPLAKAIGLEIKLCLLS

3D structure

• PDB: 4da4 Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation.
• Chain: B
• Resolution: 2.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C1229 E1269 R1313 R1315
• Catalytic site (residue number reindexed from 1): C461 E501 R545 R547
• 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	B	G1234 N1236 R1237 R1272 S1276 R1492 C1501 H1504 R1508 H1509 W1512 M1535 G1536 K1537	G466 N468 R469 R504 S508 R724 C733 H736 R740 H741 W744 M767 G768 K769
BS02	dna	B	S981 Y983 K985 P1227 P1228 C1229 Q1230 S1233 M1235 N1236 F1238 Y1243 E1269 V1271 R1314 R1315 T1527 T1530 G1536 K1537 N1580	S238 Y240 K242 P459 P460 C461 Q462 S465 M467 N468 F470 Y475 E501 V503 R546 R547 T759 T762 G768 K769 N812
BS03	SAH	B	F1148 S1149 G1150 G1153 L1154 E1171 M1172 A1581 V1582	F380 S381 G382 G385 L386 E403 M404 A813 V814
BS04	ZN	B	C1479 C1481 C1487 H1504	C711 C713 C719 H736
BS05	ZN	B	H796 C823 C897 C900	H65 C92 C154 C157

Gene Ontology

Molecular Function

• GO:0003682 chromatin binding
• GO:0008168 methyltransferase activity

External links

• PDB: RCSB:4da4, PDBe:4da4, PDBj:4da4
• PDBsum: 4da4
• PubMed: 22323818
• UniProt: P13864|DNMT1_MOUSE DNA (cytosine-5)-methyltransferase 1 (Gene Name=Dnmt1)