Structure of PDB 6kqq Chain A

Receptor sequence

>6kqqA (length=223) Species: 9606 (Homo sapiens)

NDKKPPPYKHIKVNRPIGRVQIFTADLSEIPRCNCKATDENPCGIDSECI
NRMLLYECHPTVCPAGGRCQNQCFSKRQYPEVEIFRTLQRGWGLRTKTDI
KKGEFVNEYVGELIDEEECRARIRYAQEHDITNFYMLTLDKDRIIDAGPK
GNYARFMNHCCQPNCETQKWSVNGDTRVGLFALSDIKAGTELTFNYNLEC
LGNGKTVCKCGAPNCSGFLGVRP

3D structure

• PDB: 6kqq Covalent inhibition of NSD1 histone methyltransferase.
• Chain: A
• Resolution: 1.8 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.357: [histone H3]-lysine(36) N-dimethyltransferase.

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	SAM	A	R1952 W1954 T1994 N1995 F1996 Y1997 R2017 N2020 H2021 Y2058 C2070 L2081	R90 W92 T132 N133 F134 Y135 R155 N158 H159 Y196 C208 L219
BS02	DQL	A	F1996 Y2058 C2062 L2063 G2064 G2066 K2067 T2068 G2082	F134 Y196 C200 L201 G202 G204 K205 T206 G220
BS03	DW9	A	D1864 K1865 K1866 P1867 K1871 H1872 I1946 G2010 P2011 N2014 Y2015 R2017 F2018	D2 K3 K4 P5 K9 H10 I84 G148 P149 N152 Y153 R155 F156
BS04	ZN	A	C2023 C2070 C2072 C2077	C161 C208 C210 C215
BS05	ZN	A	C1905 C1920 C1925 C1931	C43 C58 C63 C69
BS06	ZN	A	C1895 C1897 C1905 C1911	C33 C35 C43 C49
BS07	CA	A	E1978 K2003	E116 K141

Gene Ontology

Molecular Function

• GO:0042054 histone methyltransferase activity

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:6kqq, PDBe:6kqq, PDBj:6kqq
• PDBsum: 6kqq
• PubMed: 32868895
• UniProt: Q96L73|NSD1_HUMAN Histone-lysine N-methyltransferase, H3 lysine-36 specific (Gene Name=NSD1)