6G25: NSD3-PWWP1

X-ray structure of NSD3-PWWP1 in complex with compound 4. Determined by X-ray diffraction at 1.43 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 1.43 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,192
Mol. weight: 16.51 kDa
Ligands: EHQ
Released: 26 Jun 2019

Explore 6G25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G25 contains 7 α-helices and 6 β-strands across 1 chain. 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	273-276	4	1
α-helix	282-283	2
β-strand	284-288	5	1
β-strand	298-300	3	1
β-strand	306-312	7	1
β-strand	318-323	6	1
α-helix	324-326	3
β-strand	327-329	3	1
α-helix	333-335	3
α-helix	336-341	6
α-helix	362-379	18
α-helix	383-390	8
α-helix	391-393	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD3	A	protein	136	Homo sapiens	Q9BZ95 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6G25_1 Histone-lysine N-methyltransferase NSD3 (chains A)
STGVKFQVGDLVWSKVGTYPWWPCMVSSDPQLEVHTKINTRGAREYHVQFFSNQPERAWV
HEKRVREYKGHKQYEELLAEATKQASNHSEKQKIRKPRPQRERAQWDIGIAHAEKALKMT
REERIEQYTFIYIDKQ

Ligands and cofactors

ID	Name	Formula	Copies
EHQ	3,5-dimethyl-4-(4-pyridin-4-yl-1~{H}-pyrazol-3-yl)-1,2-oxazole	C13 H12 N4 O	1

Primary citation

Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Bottcher, J., Dilworth, D., Reiser, U. et al. Nat Chem Biol (2019) 15:822-829. DOI 10.1038/s41589-019-0310-x · PubMed

Other PDB entries of the same protein (UniProt Q9BZ95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
6CEN 1.61 Å, Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21
6G2B 1.61 Å, X-ray structure of NSD3-PWWP1 in complex with compound 8
6G27 1.65 Å, X-ray structure of NSD3-PWWP1 in complex with compound 5
6G29 1.7 Å, X-ray structure of NSD3-PWWP1 in complex with compound 6
4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
6G2F 1.74 Å, X-ray structure of NSD3-PWWP1 in complex with compound 16
6G2C 1.76 Å, X-ray structure of NSD3-PWWP1 in complex with compound 9
5UPD 1.8 Å, Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1…
6G2O 1.81 Å, X-ray structure of NSD3-PWWP1 in complex with compound BI-9321
6G2E 1.85 Å, X-ray structure of NSD3-PWWP1 in complex with compound 13

Browse structure collections

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