SMTL ID : 8eih.1

Cryo-EM structure of human DNMT3B homo-tetramer (form I)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

SAH.1: 13 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, R.629, S.630, W.631 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.381, A:T.383, A:E.402, A:V.403, A:D.424, A:D.424, A:V.425, A:R.629, A:W.631, A:W.631 pi-Stacking: A:F.378 SAH.5: 12 residues within 4Å: Chain B: F.378, D.379, T.383, S.401, E.402, V.403, C.404, D.424, V.425, R.629, S.630, W.631 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.381, B:T.383, B:V.403, B:D.424, B:D.424, B:V.425, B:R.629, B:W.631, B:W.631 pi-Stacking: B:F.378, B:F.378

12 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 5 residues within 4Å: Chain A: C.232, S.234, C.235, C.252, C.255 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.232, A:S.234, A:C.235, A:C.252, A:C.255 ZN.3: 5 residues within 4Å: Chain A: C.275, C.278, E.280, 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, S.234, C.235, C.252, 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: 4 residues within 4Å: Chain B: C.275, C.278, 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.9: 4 residues within 4Å: Chain C: C.232, C.235, C.252, C.255 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.232, C:C.252, C:C.255 ZN.10: 4 residues within 4Å: Chain C: C.275, C.278, C.297, C.300 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.275, C:C.278, C:C.297, C:C.300 ZN.11: 4 residues within 4Å: Chain C: C.287, C.292, C.321, C.324 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.287, C:C.292, C:C.321, C:C.324 ZN.12: 7 residues within 4Å: Chain D: C.232, L.233, S.234, G.250, L.251, C.252, C.255 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.250 ZN.13: 4 residues within 4Å: Chain D: C.275, C.278, C.297, C.300 No protein-ligand interaction detected (PLIP) ZN.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

DNA (cytosine-5)-methyltransferase 3B

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