Structure of PDB 5v21 Chain A

Receptor sequence

>5v21A (length=245) Species: 9606 (Homo sapiens)

PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERQCECTPLSKDE
RAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTE
KKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMA
LKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPS
GSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGK

3D structure

• PDB: 5v21 Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation.
• Chain: A
• Resolution: 2.415 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1579 Y1666
• Catalytic site (residue number reindexed from 1): Y121 Y208
• Enzyme Commision number: 2.1.1.-
  2.1.1.359: [histone H3]-lysine(36) N-trimethyltransferase.

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	peptide	A	Y1579 F1589 Y1604 F1606 M1607 A1608 E1636 T1637 T1653 D1665 Y1666 Q1667 F1668 Q1669 R1670 Y1671 G1672 K1673 E1674 A1700	Y121 F131 Y146 F148 M149 A150 E178 T179 T195 D207 Y208 Q209 F210 Q211 R212 Y213 G214 K215 E216 A242
BS02	ZN	A	C1516 C1529 C1539	C58 C71 C81
BS03	ZN	A	C1499 C1501 C1516 C1520	C41 C43 C58 C62
BS04	ZN	A	C1631 C1678 C1680 C1685	C173 C220 C222 C227
BS05	SAM	A	K1560 G1561 W1562 H1603 Y1604 Y1605 R1625 F1626 N1628 H1629 Y1666 Q1676 C1678 F1679	K102 G103 W104 H145 Y146 Y147 R167 F168 N170 H171 Y208 Q218 C220 F221

Gene Ontology

Molecular Function

• GO:0016279 protein-lysine N-methyltransferase activity
• GO:0042054 histone methyltransferase activity
• GO:0046975 histone H3K36 methyltransferase activity

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5v21, PDBe:5v21, PDBj:5v21
• PDBsum: 5v21
• PubMed: 28256625
• UniProt: Q9BYW2|SETD2_HUMAN Histone-lysine N-methyltransferase SETD2 (Gene Name=SETD2)