6G3P: Seleno-methionine labelled NSD3-PWWP1

X-ray structure of seleno-methionine labelled NSD3-PWWP1. Determined by X-ray diffraction at 2.8 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,067
Mol. weight: 72.28 kDa
Released: 26 Jun 2019

Explore 6G3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6G3P contains 24 α-helices and 26 β-strands across 4 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	250	1	1
α-helix	252-255	4
β-strand	273-276	4	2
β-strand	284-288	5	2
β-strand	298-300	3	2
β-strand	306-312	7	2
β-strand	319-323	5	2
α-helix	324-326	3
β-strand	327-329	3	2
α-helix	333-335	3
α-helix	336-342	7
α-helix	362-378	17
α-helix	383-390	8
α-helix	391-393	3

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	273-276	4	3
β-strand	284-288	5	3
β-strand	298-300	3	3
β-strand	306-312	7	3
β-strand	319-323	5	3
α-helix	324-326	3
β-strand	327-329	3	3
α-helix	333-335	3
α-helix	336-345	10
α-helix	350-357	8
α-helix	359-361	3
α-helix	362-378	17
α-helix	383-390	8
α-helix	391-392	2
β-strand	393	1	1

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	273-276	4	4
β-strand	284-288	5	4
β-strand	298-300	3	4
β-strand	306-312	7	4
β-strand	319-323	5	4
α-helix	324-326	3
β-strand	327-329	3	4
α-helix	335-343	9
α-helix	362-378	17
α-helix	383-389	7

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	273-276	4	5
β-strand	284-288	5	5
β-strand	298-300	3	5
β-strand	306-312	7	5
β-strand	319-323	5	5
α-helix	324-326	3
β-strand	327-329	3	5
α-helix	333-335	3
α-helix	336-342	7
α-helix	362-379	18
α-helix	383-389	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD3	A, B, C, D	protein	153	Homo sapiens	Q9BZ95 (AlphaFold model)

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

>6G3P_1 Histone-lysine N-methyltransferase NSD3 (chains A, B, C, D)
GEAPVQPILSSVPTTEVSTGVKFQVGDLVWSKVGTYPWWPCMVSSDPQLEVHTKINTRGA
REYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEKQKIRKPRPQRER
AQWDIGIAHAEKALKMTREERIEQYTFIYIDKQ

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:

6G25 1.43 Å, X-ray structure of NSD3-PWWP1 in complex with compound 4
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

Browse structure collections

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