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

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.86, K.89, W.97, T.98, V.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.97, A:V.99 Water bridges: A:D.100 EDO.2: 4 residues within 4Å: Chain A: E.340, A.343, I.344, S.345 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.340, A:S.345, A:S.345 EDO.3: 3 residues within 4Å: Chain A: K.567, N.570, L.571 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.570 EDO.4: 5 residues within 4Å: Chain A: N.399, I.432, R.433, E.437 Chain B: T.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.399, A:R.433, A:E.437 Water bridges: A:G.441 EDO.9: 5 residues within 4Å: Chain A: N.252, I.257 Chain B: T.10 Chain C: G.5, A.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.252 EDO.10: 5 residues within 4Å: Chain B: A.7, G.9, T.10 Chain C: T.8, T.9 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: G.250, A.251, N.252, V.259, S.260 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.250, A:V.259, A:S.260, H2O.5 K.6: 4 residues within 4Å: Chain A: K.89, K.90, Y.92, E.94 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.90, A:Y.92, A:E.94, H2O.7, H2O.7 K.7: 3 residues within 4Å: Chain A: L.366, V.369, D.371 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.366, A:D.371

1 x T96: N-[(4-aminophenyl)methyl]adenosine(Non-covalent)

T96.8: 16 residues within 4Å: Chain A: G.29, I.30, I.62, S.63, G.65, D.115, I.116, D.117, C.149, D.150, S.151, N.166, P.168, Y.179, F.201 Chain B: A.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.116, A:D.150, A:S.151 Water bridges: A:Y.169 pi-Stacking: A:Y.179, A:F.201

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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