SMTL ID : 7vs4.1

Crystal structure of PacII_M1M2S-DNA(m6A)-SAH complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SAH.1: 23 residues within 4Å: Chain A: E.170, F.171, Y.172, T.173, R.175, P.196, A.197, C.198, G.199, T.200, G.201, G.202, M.203, E.227, K.228, N.229, T.232, G.253, D.254, T.255, N.276, P.278, W.311 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.173, A:T.173, A:T.173, A:T.200, A:G.201, A:G.202, A:M.203, A:K.228, A:K.228, A:D.254, A:D.254, A:T.255 Water bridges: A:E.170, A:N.229, A:N.229, A:N.276, B:G.30 Salt bridges: A:R.175 pi-Stacking: A:W.311 SAH.2: 19 residues within 4Å: Chain B: A.177, A.178, E.179, F.180, Y.181, T.182, D.204, T.206, C.207, G.208, M.212, E.236, V.237, G.262, D.263, T.264, N.285, P.287, F.320 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.182, B:T.206, B:M.212, B:V.237, B:D.263, B:T.264, B:N.285 Water bridges: B:E.179, B:C.207, B:G.210, B:G.211, B:T.241, B:T.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems. Nat Commun (2022)

Release Date

2022-11-30

Peptides

Site-specific DNA-methyltransferase (adenine-specific): A
Site-specific DNA-methyltransferase (adenine-specific): B
Site-specific DNA recognition subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Site-specific DNA-methyltransferase (adenine-specific)

Site-specific DNA-methyltransferase (adenine-specific)

Site-specific DNA recognition subunit

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