SMTL ID : 6kdt.1 (2 other biounits)

Crystal structure of human DNMT3B (Q772R)-DNMT3L complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 19 residues within 4Å: Chain A: F.14, D.15, G.16, I.17, T.19, S.37, E.38, V.39, C.40, D.60, V.61, R.62, G.81, S.82, P.83, L.104, R.265, S.266, W.267 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.17, A:T.19, A:V.39, A:D.60, A:V.61, A:R.62, A:W.267, A:W.267 pi-Stacking: A:F.14 SAH.3: 18 residues within 4Å: Chain D: F.14, D.15, G.16, I.17, T.19, S.37, E.38, V.39, C.40, D.60, V.61, R.62, G.81, P.83, L.104, R.265, S.266, W.267 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.14, D:I.17, D:T.19, D:V.39, D:D.60, D:V.61, D:W.267 pi-Stacking: D:F.14

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: N.150, V.152, G.170, M.175, N.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.170, A:G.170 FMT.4: 4 residues within 4Å: Chain D: N.150, F.168, G.170, N.176 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.168, D:G.170, D:N.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, C.C. et al., Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Nucleic Acids Res. (2020)

Release Date

2020-02-19

Peptides

DNA (cytosine-5)-methyltransferase 3B: AD
DNA (cytosine-5)-methyltransferase 3-like: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

DNA (cytosine-5)-methyltransferase 3B

DNA (cytosine-5)-methyltransferase 3-like

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