SMTL ID : 5nrs.1

Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.103, R.107, P.145, N.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.146 Salt bridges: A:K.103, A:R.107 SO4.2: 3 residues within 4Å: Chain A: K.46, R.47 Chain B: H.99 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.46, A:R.47, B:H.99 SO4.4: 5 residues within 4Å: Chain A: K.16 Chain B: K.103, R.107, P.145, N.146 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.16, B:K.103, B:R.107 Hydrogen bonds: B:N.146 SO4.5: 2 residues within 4Å: Chain B: K.29, K.71 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.29, B:K.71 SO4.6: 2 residues within 4Å: Chain B: K.46, R.47 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.46, B:R.47

2 x 962: (2~{S})-1-[2-hydroxyethyl-[(2~{S})-2-oxidanylpropyl]amino]propan-2-ol(Non-covalent)

962.3: 6 residues within 4Å: Chain A: I.28, F.31, W.34, W.58, D.61, K.63 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.28, A:F.31 Salt bridges: A:D.61 962.7: 5 residues within 4Å: Chain B: I.28, F.31, W.34, W.58, D.61 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.31, B:F.31, B:W.34 Hydrogen bonds: B:D.61, B:D.61 Salt bridges: B:D.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rondelet, G. et al., Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors. To be published

Release Date

2018-05-30

Peptides

DNA (cytosine-5)-methyltransferase 3B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA (cytosine-5)-methyltransferase 3B

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