SMTL ID : 8te4.1 (1 other biounit)

Crystal structure of the methyltransferase domain of R882H/N879A DNMT3A homotetramer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: F.15, D.16, G.17, I.18, T.20, S.38, E.39, V.40, C.41, D.61, V.62, R.63, G.82, P.84, L.105, R.266, S.267, W.268 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.15, A:I.18, A:T.20, A:V.40, A:C.41, A:D.61, A:V.62, A:W.268 Water bridges: A:R.63, A:R.266 pi-Stacking: A:F.15 SAH.7: 18 residues within 4Å: Chain B: F.15, D.16, G.17, I.18, T.20, S.38, E.39, V.40, C.41, D.61, V.62, R.63, G.82, P.84, L.105, R.266, S.267, W.268 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:F.15, B:I.18, B:T.20, B:V.40, B:C.41, B:D.61, B:V.62, B:W.268 Water bridges: B:R.63, B:R.266 pi-Stacking: B:F.15

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: H.114, R.117, K.119 Chain D: K.119, E.120 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.120, A:R.117 Water bridges: A:H.114 GOL.3: 6 residues within 4Å: Chain A: S.150, G.171, N.172, L.173, G.175, M.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.150, A:G.175, A:M.176 Water bridges: A:N.151, A:N.177 GOL.4: 4 residues within 4Å: Chain A: H.164, F.202, K.204, R.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.203, A:K.204, A:K.204, A:R.206 GOL.5: 6 residues within 4Å: Chain A: H.164, R.165, A.166, R.167, R.206, T.207 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.166, A:R.167, A:R.206, A:T.207 GOL.6: 2 residues within 4Å: Chain A: R.6, E.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.6, A:R.6 Water bridges: A:K.281, A:E.282 GOL.8: 6 residues within 4Å: Chain B: H.114, R.117, K.119, E.120 Chain C: K.119, E.120 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.114, B:R.117, C:K.119, C:E.120 Water bridges: B:K.119 GOL.9: 2 residues within 4Å: Chain B: R.6, E.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.6, B:E.282, B:E.282 Water bridges: B:E.282 GOL.10: 5 residues within 4Å: Chain B: H.164, F.202, S.203, K.204, R.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.206, B:R.206 GOL.11: 5 residues within 4Å: Chain B: H.164, R.165, A.166, R.167, T.207 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.166, B:R.167, B:R.167, B:T.207 Water bridges: B:D.156, B:D.156 GOL.12: 1 residues within 4Å: Chain B: A.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J. et al., Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat Commun (2024)

Release Date

2024-03-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

DNA (cytosine-5)-methyltransferase 3A

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