SMTL ID : 8eik.1

Cryo-EM structure of human DNMT3B homo-hexamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

SAH.1: 14 residues within 4Å: Chain A: F.378, D.379, G.380, T.383, S.401, E.402, V.403, C.404, D.424, V.425, P.447, R.629, S.630, W.631 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:F.378, A:T.383, A:T.383, A:E.402, A:V.403, A:D.424, A:V.425, A:R.629, A:W.631 pi-Stacking: A:F.378 SAH.5: 12 residues within 4Å: Chain B: F.378, D.379, S.401, E.402, V.403, D.424, V.425, G.445, P.447, R.629, S.630, W.631 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.424, B:V.425, B:R.629, B:R.629, B:R.629, B:W.631 SAH.9: 14 residues within 4Å: Chain D: F.378, D.379, G.380, I.381, T.383, S.401, E.402, D.424, V.425, G.445, P.447, R.629, S.630, W.631 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.378, D:I.381, D:T.383, D:D.424, D:V.425, D:R.629, D:R.629, D:W.631

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.232, C.235, C.252, C.255 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.232, A:C.235, A:C.252, A:C.255 ZN.3: 4 residues within 4Å: Chain A: C.275, C.278, C.297, C.300 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.275, A:C.278, A:C.297, A:C.300 ZN.4: 4 residues within 4Å: Chain A: C.287, C.292, C.321, C.324 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.287, A:C.292, A:C.321, A:C.324 ZN.6: 5 residues within 4Å: Chain B: C.232, C.235, C.252, T.254, C.255 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.232, B:C.235, B:C.252, B:C.255 ZN.7: 5 residues within 4Å: Chain B: C.275, C.278, E.280, C.297, C.300 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.275, B:C.278, B:C.297, B:C.300 ZN.8: 4 residues within 4Å: Chain B: C.287, C.292, C.321, C.324 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.287, B:C.292, B:C.321, B:C.324 ZN.10: 5 residues within 4Å: Chain D: C.232, C.235, C.252, T.254, C.255 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.232, D:C.235, D:C.252, D:C.255 ZN.11: 4 residues within 4Å: Chain D: C.275, C.278, C.297, C.300 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.275, D:C.278, D:C.297, D:C.300 ZN.12: 4 residues within 4Å: Chain D: C.287, C.292, C.321, C.324 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.287, D:C.292, D:C.321, D:C.324 ZN.13: 5 residues within 4Å: Chain E: C.232, L.251, C.252, C.255, R.256 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.252 ZN.14: 5 residues within 4Å: Chain E: C.275, T.276, V.277, C.278, C.300 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.275 ZN.15: 2 residues within 4Å: Chain E: C.292, R.294 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J. et al., Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res. (2023)

Release Date

2023-09-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

E
E

F
F

DNA (cytosine-5)-methyltransferase 3B

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