SMTL ID : 6pbd.1

DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 21 residues within 4Å: Chain A: G.19, D.20, C.21, D.39, P.41, W.65, H.197, T.199, Q.200, K.201, P.223, F.224, F.225, G.226, V.227, T.229, E.245, R.246, E.247, Y.250 Chain C: A.11 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.20, A:D.20, A:C.21, A:D.39, A:W.65, A:H.197, A:T.199, A:K.201, A:F.224, A:V.227, A:G.228, A:T.229, A:R.246, A:R.246 Water bridges: A:T.229, A:R.246 Salt bridges: A:H.197 pi-Stacking: A:F.224, A:F.224 SFG.2: 19 residues within 4Å: Chain B: G.19, D.20, C.21, D.39, P.41, H.197, T.199, Q.200, K.201, P.223, F.224, F.225, G.226, V.227, T.229, E.245, R.246, E.247, Y.250 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:D.39, B:F.224 Hydrogen bonds: B:D.20, B:C.21, B:D.39, B:D.39, B:H.197, B:T.199, B:K.201, B:F.224, B:V.227, B:T.229, B:R.246 Water bridges: B:T.229 Salt bridges: B:H.197 pi-Stacking: B:F.224, B:F.224

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: G.135 Chain B: Y.157, T.158, F.159 Chain C: C.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.159, A:G.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun (2019)

Release Date

2019-10-23

Peptides

Modification methylase CcrMI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Modification methylase CcrMI