SMTL ID : 8fs2.2 (2 other biounits)

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor 11b (YD907)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.85, K.88, W.96, T.97, V.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.88, A:W.96, A:V.98 Water bridges: A:T.97, A:D.99 EDO.2: 5 residues within 4Å: Chain A: E.339, A.342, I.343, S.344 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.339, A:S.344, A:S.344 EDO.3: 3 residues within 4Å: Chain A: K.566, N.569, L.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.569 EDO.4: 4 residues within 4Å: Chain A: K.88, K.89, E.93 Ligands: K.7 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: K.158, K.209, Q.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.210 EDO.11: 5 residues within 4Å: Chain A: S.344, F.445 Chain B: C.3, A.4 Ligands: EDO.2 No protein-ligand interaction detected (PLIP)

1 x YB5: 5'-S-{3-[N'-(cyclohexylmethyl)carbamimidamido]propyl}-N-(3-phenylpropyl)-5'-thioadenosine(Non-covalent)

YB5.5: 18 residues within 4Å: Chain A: Y.30, I.61, S.62, G.64, D.114, I.115, D.116, C.148, D.149, S.150, P.167, Y.168, I.169, E.175, Y.178, L.196, F.200 Chain B: A.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.115, A:Y.178, A:L.196 Hydrogen bonds: A:I.115, A:D.116, A:D.149, A:S.150, A:Y.168 pi-Stacking: A:Y.178, A:F.200

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.6: 5 residues within 4Å: Chain A: G.249, A.250, N.251, V.258, S.259 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.249, A:V.258, A:S.259 K.7: 5 residues within 4Å: Chain A: K.88, K.89, Y.91, E.93 Ligands: EDO.4 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.365, A:D.370 K.10: 2 residues within 4Å: Chain B: T.10 Chain C: G.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile- Specific DNA Adenine Methyltransferase. Acs Chem.Biol. (2023)

Release Date

2023-05-10

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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