SMTL ID : 9gbf.2 (1 other biounit)

X-RAY structure of PHDvC5HCH tandem domain of NSD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.14, R.16, C.17, H.36, C.39 Ligands: EPE.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.14, A:C.17, A:H.36, A:C.39 ZN.2: 6 residues within 4Å: Chain A: C.26, R.28, C.31, K.33, C.52, H.55 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.31, A:C.52, A:H.55 ZN.3: 7 residues within 4Å: Chain A: C.68, L.70, C.71, N.73, C.95, E.97, H.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.68, A:C.71, A:C.95, A:H.98 ZN.4: 6 residues within 4Å: Chain A: C.57, V.59, C.60, K.62, C.76, H.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.60, A:C.76, A:H.79

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 8 residues within 4Å: Chain A: P.53, W.54, H.56, D.58, S.64, P.72, N.73, S.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.58, A:S.74, A:S.74

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 9 residues within 4Å: Chain A: C.17, D.19, G.20, G.21, Q.22, H.36, S.38, C.39 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.22 Water bridges: A:S.38 Salt bridges: A:D.19, A:H.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berardi, A. et al., The C-terminal PHDVC5HCH tandem domain of NSD2 is a combinatorial reader of unmodified H3K4 and tri-methylated H3K27 that regulates transcription of cell adhesion genes in multiple myeloma. Nucleic Acids Res. (2024)

Release Date

2024-12-18

Peptides

Histone-lysine N-methyltransferase NSD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone-lysine N-methyltransferase NSD2

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