SMTL ID : 8cy0.2 (2 other biounits)

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor MC4756 (Compound 178)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: I.84, Y.85, K.88, W.96, T.97, V.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.88, A:K.88, A:V.98 Water bridges: A:D.99 EDO.2: 4 residues within 4Å: Chain A: K.88, K.89, E.93 Ligands: K.7 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: L.297, K.298, S.299, F.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.297 Water bridges: A:H.304 EDO.4: 3 residues within 4Å: Chain A: K.43, Q.242, D.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 EDO.5: 4 residues within 4Å: Chain A: S.344, F.445 Chain B: C.3, A.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.344 EDO.10: 4 residues within 4Å: Chain A: N.251, I.256 Chain B: T.10 Chain C: G.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.256

3 x K: POTASSIUM ION(Non-covalent)

K.6: 5 residues within 4Å: Chain A: G.249, A.250, N.251, V.258, S.259 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.258, A:S.259 K.7: 5 residues within 4Å: Chain A: K.88, K.89, Y.91, E.93 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.89, A:Y.91 K.8: 3 residues within 4Å: Chain A: L.365, V.368, D.370 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.365

1 x Q9W: N-(4-phenylbutyl)adenosine(Non-covalent)

Q9W.9: 14 residues within 4Å: Chain A: G.28, I.61, S.62, G.64, D.114, I.115, D.116, C.148, D.149, S.150, P.167, Y.178, L.196, F.200 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.115, A:Y.178 Hydrogen bonds: A:I.115, A:D.149, A:S.150 pi-Stacking: A:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. J.Med.Chem. (2023)

Release Date

2023-01-11

Peptides

Site-specific DNA-methyltransferase (adenine-specific): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Site-specific DNA-methyltransferase (adenine-specific)

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