7MDN: Histone-lysine N-methyltransferase NSD2
Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a. Determined by X-ray diffraction at 2.42 Å resolution. Released 5 May 2021.
- Method
- X-ray diffraction
- Resolution
- 2.42 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 7,673
- Mol. weight
- 130.7 kDa
- Ligands
- Y6V
- Released
- 5 May 2021
Explore 7MDN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7MDN contains 53 α-helices and 48 β-strands across 8 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 | 272-277 | 6 | 1 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 1 |
| α-helix | 287-289 | 3 | |
| α-helix | 290-298 | 9 | |
| α-helix | 304-311 | 8 | |
| α-helix | 313-314 | 2 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Chains B, D and F: 7 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 |
| β-strand | 260-266 | 7 | 2 |
| 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 | 304-311 | 8 | |
| α-helix | 313-314 | 2 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Chain C: 7 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 |
| β-strand | 272-277 | 6 | 3 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 3 |
| α-helix | 287-289 | 3 | |
| α-helix | 290-299 | 10 | |
| α-helix | 304-311 | 8 | |
| α-helix | 313-314 | 2 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Chain E: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-228 | 4 | 5 |
| β-strand | 236-240 | 5 | 5 |
| β-strand | 250-253 | 4 | 5 |
| β-strand | 259-266 | 8 | 5 |
| β-strand | 272-277 | 6 | 5 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 5 |
| α-helix | 287-289 | 3 | |
| α-helix | 290-300 | 11 | |
| α-helix | 313-314 | 2 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Chain G: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-228 | 4 | 7 |
| β-strand | 236-240 | 5 | 7 |
| β-strand | 250-252 | 3 | 7 |
| β-strand | 260-266 | 7 | 7 |
| β-strand | 272-277 | 6 | 7 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 7 |
| α-helix | 287-289 | 3 | |
| α-helix | 290-300 | 11 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Chain H: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-228 | 4 | 8 |
| β-strand | 236-240 | 5 | 8 |
| β-strand | 250-252 | 3 | 8 |
| β-strand | 260-266 | 7 | 8 |
| β-strand | 272-277 | 6 | 8 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 8 |
| α-helix | 287-289 | 3 | |
| α-helix | 290-297 | 8 | |
| α-helix | 304-311 | 8 | |
| α-helix | 313-314 | 2 | |
| α-helix | 316-333 | 18 | |
| α-helix | 337-344 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone-lysine N-methyltransferase NSD2 | A, B, C, D, E, F, G, H | protein | 140 | Homo sapiens | O96028 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>7MDN_1 Histone-lysine N-methyltransferase NSD2 (chains A, B, C, D, E, F, G, H)
GRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGDA
PERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQAE
EAASMSVEERKAKFTFLYVG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| Y6V | ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazi… | C17 H16 N2 O3 S | 8 |
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.
- 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
- 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
Browse structure collections
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