SMTL ID : 1tw2.1

Crystal structure of Carminomycin-4-O-methyltransferase (DnrK) in complex with S-adenosyl-L-homocystein (SAH) and 4-methoxy-e-rhodomycin T (M-ET)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: Y.147, R.157, L.164, F.172, G.191, G.192, G.193, E.214, M.215, G.240, D.241, F.242, F.243, S.256, F.257, N.261, W.262 Ligands: ERT.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.157, A:R.157, A:G.191, A:D.241, A:F.242 Water bridges: A:S.256, A:S.256, A:S.256 pi-Stacking: A:Y.147, A:F.242 SAH.3: 19 residues within 4Å: Chain B: Y.147, R.157, L.164, F.172, G.191, G.192, G.193, E.214, M.215, G.240, D.241, F.242, F.243, S.256, F.257, V.258, N.261, W.262 Ligands: ERT.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.157, B:R.157, B:G.191, B:D.241, B:D.241, B:F.242 Water bridges: B:Y.147, B:Y.147, B:S.256, B:S.256, B:S.256 pi-Stacking: B:Y.147, B:F.242

2 x ERT: METHYL (4R)-2-ETHYL-2,5,12-TRIHYDROXY-7-METHOXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-RIBO-HEXOPYRANOSYL]OXY}-1H,2H,3H,4H,6H,11H-TETRACENE-1-CARBOXYLATE(Non-covalent)

ERT.2: 18 residues within 4Å: Chain A: W.110, V.117, F.146, Y.147, F.160, L.164, C.166, D.167, A.171, F.172, F.257, N.261, E.303, L.304, R.307, F.311, Y.346 Ligands: SAH.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.146, A:D.167, A:F.257, A:L.304, A:L.304, A:F.311, A:Y.346 Hydrogen bonds: A:N.261, A:R.307 Water bridges: A:L.164, A:D.167 Salt bridges: A:R.307 pi-Stacking: A:F.160 ERT.4: 15 residues within 4Å: Chain B: W.110, V.117, F.160, L.164, A.171, F.172, F.257, N.261, L.304, R.307, M.308, F.311, Y.346, L.348 Ligands: SAH.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.160, B:F.160, B:F.257, B:L.304, B:F.311, B:F.311, B:L.348 Hydrogen bonds: B:N.261, B:R.307 Water bridges: B:L.304 Salt bridges: B:R.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jansson, A. et al., Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products. J.Biol.Chem. (2004)

Release Date

2004-09-14

Peptides

Carminomycin 4-O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carminomycin 4-O-methyltransferase

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