SMTL ID : 8te4.2 (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 12 PLIP interactions: 12 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.262, A:R.266 pi-Stacking: A:F.15 SAH.4: 17 residues within 4Å: Chain C: F.15, D.16, G.17, I.18, T.20, S.38, E.39, V.40, C.41, D.61, V.62, G.82, P.84, L.105, R.266, S.267, W.268 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.15, C:D.16, C:I.18, C:T.20, C:V.40, C:C.41, C:D.61, C:V.62, C:W.268 Water bridges: C:R.63, C:R.266 pi-Stacking: C:F.15

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.117, K.119, E.120 Chain B: K.119, E.120 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.117, A:R.117, A:E.120, B:E.120 GOL.3: 5 residues within 4Å: Chain A: H.164, F.202, S.203, K.204, R.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.164, A:S.203, A:K.204, A:R.206 Water bridges: A:S.203 GOL.5: 5 residues within 4Å: Chain C: R.117, K.119, E.120 Chain D: K.119, E.120 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.117, C:K.119, C:E.120, D:E.120 Water bridges: C:K.119 GOL.6: 5 residues within 4Å: Chain C: S.150, N.151, G.171, L.173, M.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.150, C:N.151 GOL.7: 2 residues within 4Å: Chain C: R.6, E.282 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.6, C:R.6, C:E.282 GOL.8: 5 residues within 4Å: Chain C: H.164, F.202, S.203, K.204, R.206 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.203, C:K.204, C:R.206, C:R.206

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
C

B
H

C
D

D
G

DNA (cytosine-5)-methyltransferase 3A

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