SMTL ID : 4wxh.1

Carminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert) in complex with S-adenosyl-L-homocysteine (SAH) and aclacinomycin T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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, 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: 3VL.2 13 PLIP interactions: 13 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:S.262, A:S.262, A:S.262 pi-Stacking: A:Y.153, A:F.248 SAH.7: 17 residues within 4Å: Chain B: Y.153, R.163, L.170, F.178, G.197, G.198, E.220, M.221, G.246, D.247, F.248, F.249, S.262, F.263, N.267, W.268 Ligands: 3VL.8 14 PLIP interactions: 14 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 Water bridges: B:Y.153, B:Y.153, B:S.262, B:S.262, B:S.262 pi-Stacking: B:Y.153, B:F.248

2 x 3VL: methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate(Non-covalent)

3VL.2: 17 residues within 4Å: Chain A: W.116, V.123, F.166, L.170, C.172, D.173, A.177, F.263, N.267, F.307, E.310, L.311, R.314, M.315, F.318, I.351 Ligands: SAH.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.116, A:F.166, A:F.166, A:L.170, A:F.307, A:L.311, A:F.318, A:F.318, A:I.351 Hydrogen bonds: A:D.173, A:N.267, A:N.267, A:R.314 Water bridges: A:D.173 Salt bridges: A:R.314 3VL.8: 17 residues within 4Å: Chain B: W.116, V.123, F.166, L.170, C.172, D.173, A.177, F.178, F.263, N.267, F.307, E.310, L.311, R.314, M.315, I.351 Ligands: SAH.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.116, B:F.166, B:F.166, B:L.170, B:D.173, B:L.311, B:I.351 Hydrogen bonds: B:N.267, B:N.267, B:R.314 Water bridges: B:L.170, B:D.173 Salt bridges: B:R.314

1 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.3: 3 residues within 4Å: Chain A: P.349, T.350 Chain B: I.24 No protein-ligand interaction detected (PLIP)

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: P.269, D.270, H.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.271 Water bridges: A:D.270, A:D.270, A:H.271 Salt bridges: A:H.271 SO4.5: 2 residues within 4Å: Chain A: R.125, R.159 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.148 Salt bridges: A:R.125, A:R.159 SO4.6: 1 residues within 4Å: Chain A: R.138 No protein-ligand interaction detected (PLIP) SO4.9: 3 residues within 4Å: Chain B: P.269, D.270, H.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.270, B:H.271 Water bridges: B:H.271 Salt bridges: B:H.271 SO4.10: 2 residues within 4Å: Chain B: R.125, R.159 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.125, B:R.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grocholski, T. et al., Divergent evolution of an atypical S-adenosyl-l-methionine-dependent monooxygenase involved in anthracycline biosynthesis. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-07-29

Peptides

Carminomycin 4-O-methyltransferase DnrK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carminomycin 4-O-methyltransferase DnrK