SMTL ID : 6u8w.1

Crystal structure of DNMT3B(K777A)-DNMT3L in complex with CpGpT DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: F.19, D.20, G.21, I.22, T.24, S.42, E.43, V.44, C.45, D.65, V.66, R.67, G.86, P.88, L.109, R.270, S.271, W.272 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.19, A:I.22, A:T.24, A:V.44, A:D.65, A:V.66, A:R.270, A:W.272 pi-Stacking: A:F.19 SAH.3: 18 residues within 4Å: Chain D: F.19, D.20, G.21, I.22, T.24, S.42, E.43, V.44, C.45, D.65, V.66, R.67, G.86, P.88, L.109, R.270, S.271, W.272 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.19, D:I.22, D:T.24, D:V.44, D:D.65, D:V.66, D:W.272 pi-Stacking: D:F.19

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: C.154, N.155, G.175, M.180 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain D: C.154, N.155, V.157, G.175, M.180 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, L. et al., Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun (2020)

Release Date

2020-06-10

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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