SMTL ID : 6kdp.1

Crystal structure of human DNMT3B-DNMT3L complex (II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-2-2-mer

Ligands

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

FMT.1: 3 residues within 4Å: Chain A: C.149, N.150, G.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.170 FMT.3: 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

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

SAH.2: 17 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, G.81, P.83, L.104, R.265, S.266, W.267 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.14, A:I.17, A:T.19, A:V.39, A:D.60, A:V.61, A:R.265, A:W.267 pi-Stacking: A:F.14 SAH.4: 19 residues within 4Å: Chain D: F.14, D.15, G.16, I.17, T.19, S.37, E.38, V.39, C.40, N.59, D.60, V.61, R.62, G.81, P.83, L.104, R.265, S.266, W.267 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:I.17, D:T.19, D:V.39, D:D.60, D:V.61, D:R.62, D:W.267, D:W.267 Water bridges: D:S.43, D:R.265 pi-Stacking: D:F.14

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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