6XCG: Histone-lysine N-methyltransferase NSD2

Name: PDB 6XCG: Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934
Published: 2020-07-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934. Determined by X-ray diffraction at 1.64 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,893
Mol. weight: 49.77 kDa
Ligands: V01
Released: 22 Jul 2020

Explore 6XCG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XCG contains 28 α-helices and 18 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	1
β-strand	236-240	5	1
β-strand	250-252	3	1
α-helix	253-255	3
β-strand	260-266	7	1
α-helix	267	1
β-strand	272-277	6	1
α-helix	278-280	3
β-strand	281-283	3	1
α-helix	287-289	3
α-helix	290-300	11
α-helix	304-310	7
α-helix	312-315	4
α-helix	316-333	18
α-helix	337-344	8
α-helix	345-347	3

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	2
β-strand	236-240	5	2
β-strand	250-252	3	2
α-helix	253-255	3
β-strand	260-266	7	2
α-helix	267	1
β-strand	272-277	6	2
α-helix	278-280	3
β-strand	281-283	3	2
α-helix	287-289	3
α-helix	290-300	11
α-helix	304-310	7
α-helix	316-333	18
α-helix	337-344	8
α-helix	345-347	3

Chain C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	3
β-strand	236-240	5	3
β-strand	250-252	3	3
β-strand	260-266	7	3
α-helix	267	1
β-strand	272-277	6	3
α-helix	278-280	3
β-strand	281-283	3	3
α-helix	287-289	3
α-helix	290-300	11
α-helix	304-311	8
α-helix	312-315	4
α-helix	316-333	18
α-helix	337-344	8
α-helix	345-347	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A, B, C	protein	141	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6XCG_1 Histone-lysine N-methyltransferase NSD2 (chains A, B, C)
GGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGD
APERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQA
EEAASMSVEERKAKFTFLYVG

Ligands and cofactors

ID	Name	Formula	Copies
V01	N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro…	C24 H21 N5 O4	3

Water and common crystallization additives (UNX) are not listed.

Primary citation

A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization. Dilworth, D., Hanley, R.P., Ferreira de Freitas, R. et al. Nat Chem Biol (2022) 18:56-63. DOI 10.1038/s41589-021-00898-0 · PubMed

Other PDB entries of the same protein (UniProt O96028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FOC 1.62 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 11.
9EXY 1.7 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 34.
9GBF 1.76 Å, X-RAY structure of PHDvC5HCH tandem domain of NSD2
5VC8 1.8 Å, Crystal structure of the WHSC1 PWWP1 domain
9KNB 1.84 Å, NSD2-PWWP1 domain bound with compound 9
9EXX 1.94 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 18.
9FOE 1.96 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 7.
9KN9 2.0 Å, NSD2-PWWP1 domain bound with compound 1.
9Y60 2.02 Å, Crystal structure of NSD2 PWWP1 domain in complex with (6R)-6-(3,5-dichlorophenyl)morphol…
5LSU 2.14 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7LMT 2.27 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a
6UE6 2.4 Å, PWWP1 domain of NSD2 in complex with MR837

Browse structure collections

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