SMTL ID : 5mgz.1

Streptomyces Spheroides NovO (8-demethylnovbiocic acid methyltransferase) with SAH

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: 22 residues within 4Å: Chain A: E.4, A.5, I.6, F.14, Y.25, C.47, C.48, G.49, D.70, L.71, S.72, M.75, G.95, D.96, A.97, Q.98, R.116, N.117, A.118, R.121, L.122 Ligands: ACT.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.14 Hydrogen bonds: A:I.6, A:Y.25, A:C.47, A:G.49, A:L.71, A:S.72, A:D.96, A:D.96, A:A.97 Water bridges: A:Y.25, A:G.51, A:R.116 Salt bridges: A:R.116 SAH.4: 21 residues within 4Å: Chain B: E.4, A.5, I.6, F.14, Y.25, C.47, C.48, G.49, D.70, L.71, S.72, M.75, G.95, D.96, A.97, Q.98, R.116, N.117, A.118, R.121, L.122 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.14 Hydrogen bonds: B:E.4, B:I.6, B:Y.25, B:C.47, B:G.49, B:L.71, B:S.72, B:D.96, B:A.97, B:Q.98 Water bridges: B:Y.25, B:G.51, B:R.116 Salt bridges: B:R.116

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: F.14, R.24, R.116, N.117, W.178, Y.216 Ligands: ACT.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.116, A:Y.216 Water bridges: A:R.116, A:M.174

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain A: N.117, H.120, R.121, F.147, W.178, A.181 Ligands: SAH.1, GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.147 Salt bridges: A:H.120, A:R.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sadler, J.C. et al., Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO. ACS Chem. Biol. (2017)

Release Date

2017-01-18

Peptides

8-demethylnovobiocic acid C(8)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

8-demethylnovobiocic acid C(8)-methyltransferase