SMTL ID : 4x7v.1

MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with Mg, SAH and mycinamicin IV (product)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 21 residues within 4Å: Chain A: T.75, M.76, I.77, E.103, G.105, V.106, W.107, A.111, D.133, S.134, G.137, F.138, P.139, L.163, G.189, W.190, F.191, D.209, G.210, D.211 Ligands: MIV.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.107 Hydrogen bonds: A:T.75, A:M.76, A:G.105, A:V.106, A:W.107, A:A.111, A:S.134, A:G.137, A:F.191, A:R.207, A:D.209 Water bridges: A:G.109, A:G.109, A:D.133, A:L.163, A:K.192, A:S.212, A:D.218 pi-Stacking: A:W.190, A:F.191 SAH.4: 21 residues within 4Å: Chain B: T.75, M.76, I.77, E.103, G.105, V.106, W.107, A.111, D.133, S.134, G.137, F.138, P.139, L.163, G.189, W.190, F.191, D.209, G.210, D.211 Ligands: MIV.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.107 Hydrogen bonds: B:M.76, B:E.103, B:G.105, B:V.106, B:W.107, B:A.111, B:S.134, B:G.137, B:F.191, B:R.207 Water bridges: B:G.109, B:D.133, B:L.163, B:K.192, B:S.212, B:A.215, B:D.218 pi-Stacking: B:W.190, B:F.191

2 x MIV: MYCINAMICIN IV(Non-covalent)

MIV.2: 17 residues within 4Å: Chain A: A.50, Y.69, M.76, R.81, M.152, L.154, Y.157, D.209, D.211, D.236, D.237, C.239, I.240, P.241, Q.266 Ligands: SAH.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.50, A:Y.69, A:L.154, A:Y.157, A:Y.157 Hydrogen bonds: A:R.81, A:Q.266 Water bridges: A:L.52, A:Y.69, A:Y.69, A:R.81 MIV.5: 18 residues within 4Å: Chain B: A.50, G.51, Y.69, M.76, R.81, M.152, L.154, Y.157, D.209, D.211, D.236, D.237, C.239, I.240, P.241, Q.266 Ligands: SAH.4, MG.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.50, B:Y.157, B:Y.157, B:I.240, B:I.240 Hydrogen bonds: B:Y.69, B:R.81, B:Q.266 Water bridges: B:L.52, B:R.81

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.209, D.211, D.236, D.237 Ligands: MIV.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.209, A:D.236, A:D.237, H2O.15 MG.6: 5 residues within 4Å: Chain B: D.209, D.211, D.236, D.237 Ligands: MIV.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.209, B:D.236, B:D.237, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernard, S.M. et al., Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O-Methyltransferases. Acs Chem.Biol. (2015)

Release Date

2015-03-04

Peptides

Mycinamicin III 3''-O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mycinamicin III 3''-O-methyltransferase

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