SMTL ID : 8te1.1 (1 other biounit)

Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 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 9 PLIP interactions: 9 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 pi-Stacking: A:F.15 SAH.6: 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.266, B:R.266 pi-Stacking: B:F.15

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.171, N.172, L.173, G.175 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.173, A:G.175 GOL.3: 7 residues within 4Å: Chain A: S.150, N.151, V.153, F.169, G.171, M.176 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.150, A:N.151, A:G.171 GOL.4: 2 residues within 4Å: Chain A: R.274, A.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.274 Water bridges: A:A.181, A:H.275, A:H.275 GOL.5: 2 residues within 4Å: Chain A: R.6, E.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.6, A:R.6 GOL.7: 4 residues within 4Å: Chain B: K.26, Q.31, V.32, K.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.32, B:K.55 Water bridges: B:K.26 GOL.8: 4 residues within 4Å: Chain B: G.171, N.172, L.173, M.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.172

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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