SMTL ID : 7v0e.2 (1 other biounit)

Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.27 Å

Oligo State

homo-tetramer

Ligands

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

SAH.1: 15 residues within 4Å: Chain A: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, G.80, R.264, S.265, W.266 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.15, A:I.16, A:T.18, A:V.38, A:D.59, A:V.60, A:W.266 pi-Stacking: A:F.13 SAH.2: 17 residues within 4Å: Chain B: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, R.61, L.103, E.129, R.264, S.265, W.266 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.16, B:V.38, B:D.59, B:V.60, B:R.264, B:W.266 pi-Stacking: B:F.13 SAH.3: 15 residues within 4Å: Chain C: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, G.80, R.264, S.265, W.266 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.15, C:I.16, C:T.18, C:C.39, C:D.59, C:V.60, C:W.266 SAH.4: 17 residues within 4Å: Chain D: F.13, D.14, G.15, I.16, T.18, S.36, E.37, V.38, C.39, D.59, V.60, P.82, L.103, E.129, R.264, S.265, W.266 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.16, D:T.18, D:V.38, D:D.59, D:V.60, D:R.61, D:R.264, D:R.264, D:W.266 pi-Stacking: D:F.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, L. et al., Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations. Nat Commun (2022)

Release Date

2022-06-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
G

D
H

DNA (cytosine-5)-methyltransferase 3B

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