- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-2-2-2-2-mer
- Ligands
- 6 x ZN: ZINC ION(Non-covalent)
ZN.1: 4 residues within 4Å:- Chain K: C.271, C.274, C.291, C.294
4 PLIP interactions:4 interactions with chain K- Metal complexes: K:C.271, K:C.274, K:C.291, K:C.294
ZN.2: 4 residues within 4Å:- Chain K: C.314, C.317, C.336, C.339
4 PLIP interactions:4 interactions with chain K- Metal complexes: K:C.314, K:C.317, K:C.336, K:C.339
ZN.3: 4 residues within 4Å:- Chain K: C.326, C.331, C.360, C.363
4 PLIP interactions:4 interactions with chain K- Metal complexes: K:C.326, K:C.331, K:C.360, K:C.363
ZN.5: 4 residues within 4Å:- Chain L: C.96, C.99, C.118, C.121
4 PLIP interactions:4 interactions with chain L- Metal complexes: L:C.96, L:C.99, L:C.118, L:C.121
ZN.6: 4 residues within 4Å:- Chain L: C.108, C.113, C.142, C.145
4 PLIP interactions:4 interactions with chain L- Metal complexes: L:C.108, L:C.113, L:C.142, L:C.145
ZN.7: 5 residues within 4Å:- Chain L: C.53, C.55, C.56, C.73, C.76
4 PLIP interactions:4 interactions with chain L- Metal complexes: L:C.53, L:C.56, L:C.73, L:C.76
- 2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
SAH.4: 18 residues within 4Å:- Chain K: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, C.443, G.462, D.463, V.464, G.484, P.486, L.507, R.668, S.669, W.670
10 PLIP interactions:10 interactions with chain K- Hydrogen bonds: K:F.417, K:I.420, K:T.422, K:V.442, K:V.464, K:R.465, K:R.668, K:R.668, K:W.670
- pi-Stacking: K:F.417
SAH.8: 15 residues within 4Å:- Chain M: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, C.443, V.464, G.484, L.507, R.668, S.669, W.670
8 PLIP interactions:8 interactions with chain M- Hydrogen bonds: M:F.417, M:I.420, M:T.422, M:V.442, M:V.464, M:W.670
- pi-Stacking: M:F.417, M:F.417
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yan, Y. et al., Structural Insights into DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin. To Be Published
- Release Date
- 2025-10-08
- Peptides
- Histone H3.2: AE
Histone H4: BF
Histone H2A type 1: CG
Histone H2B 1.1: DH
DNA (cytosine-5)-methyltransferase 3A: KM
DNA (cytosine-5)-methyltransferase 3-like: LN - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
HK
MM
KL
NN
L
SMTL ID : 9mpp.1
The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Histone H3.2
Histone H4
Histone H2A type 1
Histone H2B 1.1
DNA (cytosine-5)-methyltransferase 3A
DNA (cytosine-5)-methyltransferase 3-like
Related Entries With Identical Sequence
1eqz.1 | 1f66.1 | 1hq3.1 | 1kx3.1 | 1kx4.1 | 1kx5.1 | 1s32.1 | 1tzy.1 | 1u35.1 | 1zbb.1 | 2aro.1 | 2cv5.1 | 2f8n.1 | 2fj7.1 | 2nzd.1 | 3b6f.1 | 3b6g.1 | 3c1b.1 | 3kuy.1 | 3kxb.1 | 3lja.1 | 3lz0.1 | 3lz1.1 | 3mgp.1 | 3mgq.1 | 3mgr.1 | 3mgs.1 | 3mnn.1 | 3mvd.1 | 3nqu.1 more...less...3o62.1 | 3r45.1 | 3reh.1 | 3rei.1 | 3rej.1 | 3rek.1 | 3rel.1 | 3tu4.1 | 3tu4.2 | 3ut9.1 | 3uta.1 | 3utb.1 | 4hga.1 | 4j8u.1 | 4j8v.1 | 4j8v.2 | 4j8v.3 | 4j8w.1 | 4j8x.1 | 4j8x.2 | 4j8x.3 | 4kgc.1 | 4ld9.1 | 4r8p.1 | 4wu8.1 | 4wu9.1 | 4xuj.1 | 4z2m.1 | 4zux.1 | 4zux.2 | 5c3i.1 | 5c3i.2 | 5c3i.3 | 5c3i.4 | 5c3i.5 | 5c3i.6 | 5cp6.1 | 5dnm.1 | 5dnn.1 | 5e5a.1 | 5f99.1 | 5hq2.1 | 5kgf.1 | 5nl0.1 | 5nl0.2 | 5o9g.1 | 5omx.1 | 5ong.1 | 5onw.1 | 5oxv.1 | 5oy7.1 | 5x0x.1 | 5x0y.1 | 5xf3.1 | 5xf4.1 | 5xf5.1 | 5xf6.1 | 5z3l.1 | 5z3o.1 | 5z3u.1 | 5z3v.1 | 6buz.1 | 6e0c.1 | 6e0p.1 | 6esf.1 | 6esg.1 | 6esh.1 | 6esi.1 | 6ftx.1 | 6g0l.1 | 6hts.1 | 6i84.1 | 6iro.1 | 6j99.1 | 6jyl.1 | 6k1p.1 | 6kiu.1 | 6kiv.1 | 6kiw.1 | 6kix.1 | 6kiz.1 | 6kw3.1 | 6kw4.1 | 6kw5.1 | 6l9z.1 | 6la2.1 | 6la8.1 | 6la9.1 | 6lab.1 | 6ler.1 | 6ler.2 | 6ltj.1 | 6m3v.1 | 6m44.1 | 6m4d.1 | 6m4g.1 | 6m4h.1 | 6n1z.1 | 6n1z.2 | 6ne3.1 | 6nj9.1 | 6nn6.1 | 6nog.1 | 6nqa.1 | 6nzo.1 | 6o1d.1 | 6o22.1 | 6o96.1 | 6om3.1 | 6om3.2 | 6pa7.1 | 6pwv.1 | 6pww.1 | 6pwx.1 | 6px1.1 | 6px3.1 | 6r0c.1 | 6r1u.1 | 6r25.1 | 6r8y.1 | 6rny.1 | 6ryr.1 | 6ryu.1 | 6s01.1 | 6se0.1 | 6se6.1 | 6see.1 | 6sef.1 | 6seg.1 | 6t79.1 | 6t7a.1 | 6t7b.1 | 6t7c.1 | 6t7d.1 | 6t9l.1 | 6tda.1 | 6tem.1 | 6upk.1 | 6upl.1 | 6uxw.1 | 6v92.1 | 6ven.1 | 6vyp.1 | 6vyp.2 | 6vz4.1 | 6w5i.1 | 6w5m.1 | 6w5n.1 | 6wkr.1 | 6wz5.1 | 6wz9.1 | 6x0n.1 | 6y5d.1 | 6zhx.1 | 6zhy.1 | 7at8.1 | 7cro.1 | 7crp.1 | 7crq.1 | 7crr.1 | 7dbp.1 | 7e8i.1 | 7eg6.1 | 7egp.1 | 7enn.1 | 7jo9.1 | 7joa.1 | 7k5x.1 | 7k5y.1 | 7k60.1 | 7k61.1 | 7k63.1 | 7kbd.1 | 7kbe.1 | 7kbf.1 | 7m1x.1 | 7mbm.1 | 7mbn.1 | 7nkx.1 | 7nky.1 | 7nl0.1 | 7oh9.1 | 7oha.1 | 7ohb.1 | 7ohc.1 | 7otq.1 | 7pet.1 | 7peu.1 | 7pev.1 | 7pew.1 | 7pex.1 | 7pey.1 | 7pez.1 | 7pf0.1 | 7pf2.1 | 7pf3.1 | 7pf4.1 | 7pf5.1 | 7pf6.1 | 7pfa.1 | 7pfc.1 | 7pfd.1 | 7pfe.1 | 7pff.1 | 7pft.1 | 7pfu.1 | 7pfv.1 | 7pfw.1 | 7pfx.1 | 7pii.1 | 7r5r.1 | 7ssa.1 | 7swy.1 | 7tan.1 | 7tn2.1 | 7u0g.1 | 7u0i.1 | 7u0j.1 | 7u46.1 | 7u47.1 | 7u4d.1 | 7ud5.1 | 7unc.1 | 7und.1 | 7unk.1 | 7ux9.1 | 7v90.1 | 7v96.1 | 7v9c.1 | 7v9j.1 | 7v9k.1 | 7v9s.1 | 7va4.1 | 7vcq.1 | 7vcq.2 | 7vcq.3 | 7vdt.1 | 7vdv.1 | 7vvu.1 | 7vvz.1 | 7x3t.1 | 7x3v.1 | 7x3w.1 | 7x3x.1 | 7xfc.1 | 7xfh.1 | 7xfi.1 | 7xfj.1 | 7xfl.1 | 7xfm.1 | 7xfn.1 | 7xnp.1 | 7xpx.1 | 7y5u.1 | 7y5v.1 | 7y5w.1 | 7y60.1 | 7y61.1 | 7yi1.1 | 7yi4.1 | 7yi5.1 | 7ywx.1 | 7yyh.1 | 7zi4.1 | 7zs9.1 | 7zsa.1 | 7zsb.1 | 8a3y.1 | 8aag.1 | 8b0a.1 | 8bvw.1 | 8byq.1 | 8bz1.1 | 8cbn.1 | 8cbq.1 | 8ceo.1 | 8cww.1 | 8cze.1 | 8dk5.1 | 8du4.1 | 8ett.1 | 8etv.1 | 8eu2.1 | 8eue.1 | 8euj.1 | 8evg.1 | 8evh.1 | 8evi.1 | 8evj.1 | 8f86.1 | 8g6g.1 | 8g6h.1 | 8g6q.1 | 8g6s.1 | 8g86.1 | 8g88.1 | 8g8b.1 | 8g8g.1 | 8gpn.1 | 8h1t.1 | 8hxy.1 | 8hxz.1 | 8hy0.1 | 8ihm.1 | 8iht.1 | 8iqf.1 | 8iqg.1 | 8j6s.1 | 8j6t.1 | 8jh2.1 | 8jh3.1 | 8jh4.1 | 8jho.1 | 8kd2.1 | 8kd3.1 | 8kd4.1 | 8kd5.1 | 8kd6.1 | 8kd7.1 | 8of4.1 | 8off.1 | 8pc5.1 | 8pc6.1 | 8peo.1 | 8pep.1 | 8pki.1 | 8pkj.1 | 8rbx.1 | 8rup.1 | 8ruq.1 | 8siy.1 | 8skz.1 | 8sps.1 | 8spu.1 | 8svf.1 | 8syp.1 | 8t3t.1 | 8t3w.1 | 8t3y.1 | 8t9f.1 | 8t9g.1 | 8t9h.1 | 8tas.1 | 8tb9.1 | 8thu.1 | 8tof.1 | 8u5h.1 | 8uw1.1 | 8uxq.1 | 8v25.1 | 8v26.1 | 8v27.1 | 8v28.1 | 8v4y.1 | 8v6v.1 | 8v7l.1 | 8vfx.1 | 8vfy.1 | 8vfz.1 | 8vg0.1 | 8vg1.1 | 8vg2.1 | 8vmj.1 | 8vmn.1 | 8vob.1 | 8vx5.1 | 8vx6.1 | 8w9d.1 | 8w9e.1 | 8w9f.1 | 8x15.1 | 8x19.1 | 8x1c.1 | 8xjv.48 | 8xjv.49 | 8xjv.50 | 8xjv.51 | 8xjv.52 | 8xjv.53 | 8xjv.54 | 8xjv.55 | 8xjv.56 | 8xjv.57 | 8xjv.58 | 8xjv.59 | 8xjv.60 | 8xjv.61 | 8xjv.62 | 8xjv.63 | 8xjv.64 | 8xjv.65 | 8xjv.66 | 8xjv.67 | 8xjv.68 | 8xjv.69 | 8xjv.70 | 8xjv.71 | 8yjf.1 | 8yjm.1 | 8yti.1 | 8z50.1 | 9b2s.1 | 9b2t.1 | 9b3p.1 | 9c9g.1 | 9c9s.1 | 9c9t.1 | 9c9x.1 | 9ca7.1 | 9ca8.1 | 9caa.1 | 9cab.1 | 9can.1 | 9cau.1 | 9cb7.1 | 9cg9.1 | 9dby.1 | 9dde.1 | 9dg3.1 | 9dgg.1 | 9e1l.1 | 9e1m.1 | 9e1n.1 | 9e1o.1 | 9e1p.1 | 9e1q.1 | 9e1r.1 | 9e1u.1 | 9e1v.1 | 9e1w.1 | 9e1x.1 | 9e1y.1 | 9egx.1 | 9egy.1 | 9egz.1 | 9eh0.1 | 9eh1.1 | 9eh2.1 | 9eil.1 | 9fgq.1 | 9fh9.1 | 9gd0.1 | 9gd1.1 | 9gd2.1 | 9gd3.1 | 9gmk.1 | 9gmr.1 | 9ii7.1 | 9j0n.1 | 9j0o.1 | 9j0p.1 | 9jao.1 | 9jnp.1 | 9jnt.1 | 9jnu.1 | 9jnv.1 | 9jnw.1 | 9jnx.1 | 9jnz.1 | 9jo2.1 | 9jo5.1 | 9liu.1 | 9mp0.1 | 9mpo.1 | 9nh8.1 | 9ny4.1 | 9qaj.1 | 9rzc.1 | 9s0u.1 | 9si3.1 | 9si9.1 | 9sj5.1 | 9slj.1