› 6kqq

X-ray diffraction
1.8Å resolution

NSD1 SET domain in complex with BT3 and SAM

Released:
DOI: 10.2210/pdb6kqq/pdb
PDB entry 6kqq coloured by chain, front view.
PDB entry 6kqq coloured by chain, side view.
PDB entry 6kqq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Covalent inhibition of NSD1 histone methyltransferase.
Huang H, Howard CA, Zari S, Cho HJ, Shukla S, Li H, Ndoj J, González-Alonso P, Nikolaidis C, Abbott J, Rogawski DS, Potopnyk MA, Kempinska K, Miao H, Purohit T, Henderson A, Mapp A, Sulis ML, Ferrando A, Grembecka J, Cierpicki T
OpenAccess logo Nat Chem Biol 16 1403-1410 (2020)
PMID: 32868895

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188606 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase, H3 lysine-36 specific Chains: A, B
Molecule details ›
Chains: A, B
Length: 223 amino acids
Theoretical weight: 25.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96L73 (Residues: 1863-2085; Coverage: 8%)
Gene names: ARA267, KMT3B, NSD1
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand SAM 2 x SAM
Ligand DQL 2 x DQL
Ligand DW9 1 x DW9
Ligand ZN 6 x ZN
Ligand CA 2 x CA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P1
Unit cell:
a: 40.469Å b: 60.811Å c: 64.255Å
α: 101.182° β: 107.756° γ: 93.585°
R-values:
R R work R free
0.165 0.163 0.201
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Drug Resistance Mechanisms of Acute Myeloid Leukemia Stem Cells.
Niu et al. (2022)
12 more

2 mentions without citation

The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors.
Topchu et al. (2022)
1 more