7LMT: Histone-lysine N-methyltransferase NSD2
Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a. Determined by X-ray diffraction at 2.27 Å resolution. Released 10 Mar 2021.
- Method
- X-ray diffraction
- Resolution
- 2.27 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 7,678
- Mol. weight
- 130.7 kDa
- Ligands
- Y6V
- Released
- 10 Mar 2021
Explore 7LMT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7LMT contains 58 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: 8 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 | |
| α-helix | 345-347 | 3 | |
Chains B and F: 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 |
| 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 | |
| α-helix | 345-347 | 3 | |
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 D: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 225-228 | 4 | 4 |
| β-strand | 236-240 | 5 | 4 |
| β-strand | 250-252 | 3 | 4 |
| β-strand | 260-266 | 7 | 4 |
| β-strand | 272-277 | 6 | 4 |
| α-helix | 278-280 | 3 | |
| β-strand | 281-283 | 3 | 4 |
| 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 E: 7 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 | |
| α-helix | 345-347 | 3 | |
Chain G: 6 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 | |
| α-helix | 345-347 | 3 | |
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
>7LMT_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
Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a. Lei, M., Freitas, R.F., Dong, A. et al. To be published.
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…
- 6UE6 2.4 Å, PWWP1 domain of NSD2 in complex with MR837
Browse structure collections
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