5VC8: WHSC1 PWWP1 domain

Crystal structure of the WHSC1 PWWP1 domain. Determined by X-ray diffraction at 1.8 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 2,860
Mol. weight: 44.13 kDa
Released: 28 Jun 2017

Explore 5VC8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VC8 contains 15 α-helices and 12 β-strands across 2 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, 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
β-strand	260-266	7	1
β-strand	273-277	5	1
α-helix	278-280	3
β-strand	281-283	3	1
α-helix	287-289	3
α-helix	290-300	11
α-helix	304-311	8
α-helix	313-315	3
α-helix	316-333	18
α-helix	337-344	8

Chain B: 8 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
β-strand	273-277	5	2
α-helix	278-280	3
β-strand	281-283	3	2
α-helix	287-289	3
α-helix	290-299	10
α-helix	313-314	2
α-helix	316-333	18
α-helix	337-343	7
α-helix	345-348	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A, B	protein	141	Homo sapiens	O96028 (AlphaFold model)
dodeca-2-deoxy-nucleotide, poorly resolved by electron density	W, X, Y	DNA	12	synthetic construct
DNA (5'-d(pcptp*(dn))-3')	Z	DNA	3	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5VC8_1 Histone-lysine N-methyltransferase NSD2 (chains A, B)
GGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGD
APERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQA
EEAASMSVEERKAKFTFLYVG

Sequence of entity 2 (W, X, Y), FASTA

>5VC8_2 dodeca-2-deoxy-nucleotide, poorly resolved by electron density (chains W, X, Y)
GAGATCGATCTC

Sequence of entity 3 (Z), FASTA

>5VC8_3 DNA (5'-D(P*CP*TP*(DN))-3') (chains Z)
CTN

Primary citation

Histone and DNA binding ability studies of the NSD subfamily of PWWP domains. Zhang, M., Yang, Y., Zhou, M. et al. Biochem Biophys Res Commun (2021) 569:199-206. DOI 10.1016/j.bbrc.2021.07.017 · 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.
6XCG 1.64 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934
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
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

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