SMTL ID : 7pga.1 (1 other biounit)

Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: Y.153, R.163, M.170, F.178, G.197, G.198, G.199, E.220, M.221, G.246, D.247, F.248, S.262, F.263, N.267, W.268 Ligands: VAK.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.163, A:R.163, A:G.197, A:D.247, A:D.247, A:F.248, A:S.262 Water bridges: A:D.167, A:D.167, A:S.262 pi-Stacking: A:Y.153, A:F.248 SAH.3: 19 residues within 4Å: Chain B: Y.153, R.163, F.166, M.170, F.178, G.197, G.198, G.199, E.220, M.221, G.246, D.247, F.248, F.249, S.262, F.263, N.267, W.268 Ligands: VAK.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.163, B:R.163, B:G.197, B:D.247, B:D.247, B:F.248, B:S.262 pi-Stacking: B:Y.153, B:F.248

2 x VAK: methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate(Non-covalent)

VAK.2: 18 residues within 4Å: Chain A: W.116, V.123, F.152, Y.153, F.166, M.170, F.263, N.267, F.307, L.310, L.311, R.314, M.315, F.318, V.352, P.353, L.354 Ligands: SAH.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.116, A:F.152, A:F.166, A:L.311, A:L.311, A:L.311, A:F.318, A:F.318, A:L.354 Hydrogen bonds: A:Y.153, A:N.267, A:R.314 Salt bridges: A:R.314 VAK.4: 13 residues within 4Å: Chain B: W.116, V.123, F.166, M.170, F.263, N.267, F.307, L.310, L.311, R.314, M.315, L.354 Ligands: SAH.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.116, B:F.166, B:L.311, B:L.311 Hydrogen bonds: B:N.267, B:N.267, B:R.314 Salt bridges: B:R.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dinis, P. et al., Evolution-inspired engineering of anthracycline methyltransferases. Pnas Nexus (2023)

Release Date

2022-08-24

Peptides

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB

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