SMTL ID : 9j56.1

Functional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: W.146, M.163, G.190, G.191, G.192, E.213, L.214, P.217, G.239, D.240, F.241, F.242, S.255, F.256, N.260, W.261 Ligands: 01.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.190, A:G.192, A:L.214, A:D.240, A:D.240, A:F.241, A:S.255 Water bridges: A:S.255, A:S.255, A:S.255 pi-Stacking: A:W.146, A:F.241 SAH.3: 17 residues within 4Å: Chain B: W.146, G.190, G.191, G.192, M.196, E.213, L.214, P.217, G.239, D.240, F.241, F.242, S.255, F.256, N.260, W.261 Ligands: 01.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.190, B:G.192, B:L.214, B:D.240, B:D.240, B:F.241, B:S.255 Water bridges: B:S.255, B:S.255, B:S.255, B:N.260 pi-Stacking: B:W.146, B:F.241

2 x 01: (7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7~{H}-tetracene-5,12-dione

01.2: 19 residues within 4Å: Chain A: W.109, V.116, F.145, W.146, F.159, M.163, D.168, A.170, F.256, N.260, F.300, L.304, R.307, M.308, F.311, M.312, L.344, F.346 Ligands: SAH.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.145, A:F.159, A:A.170, A:F.256, A:F.300, A:L.304, A:L.304, A:F.311, A:F.346 Hydrogen bonds: A:M.163, A:N.260, A:R.307, A:R.307 pi-Stacking: A:W.109 01.4: 18 residues within 4Å: Chain B: W.109, V.116, F.145, W.146, F.159, M.163, F.256, N.260, F.300, L.303, L.304, R.307, M.308, F.311, M.312, L.344, F.346 Ligands: SAH.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.109, B:F.145, B:F.300, B:L.303, B:L.304, B:L.304, B:F.311, B:F.346, B:F.346 Hydrogen bonds: B:R.307, B:R.307 pi-Stacking: B:F.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sang, M. et al., Functional investigation of the SAM-dependent methyltransferase RdmB in anthracycline biosynthesis. Synth Syst Biotechnol (2025)

Release Date

2024-11-06

Peptides

Aclacinomycin 10-hydroxylase RdmB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aclacinomycin 10-hydroxylase RdmB

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