SMTL ID : 4x7z.1

MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A variant) in complex with Mg, SAH and mycinamicin III (substrate)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 22 residues within 4Å: Chain A: T.75, A.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, A.215 Ligands: ZM3.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.107 Hydrogen bonds: A:T.75, A:A.76, A:G.105, A:V.106, A:W.107, A:A.111, A:S.134, A:G.137, A:F.191, A:D.209 Water bridges: A:G.109, A:G.109, A:G.109, A:D.133, A:L.163, A:K.192, A:S.212, A:S.212, A:D.218 pi-Stacking: A:W.190, A:F.191 SAH.7: 21 residues within 4Å: Chain B: T.75, A.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: ZM3.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.107 Hydrogen bonds: B:A.76, B:I.77, 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:G.109, B:G.109, B:G.109, B:D.133, B:L.163, B:K.192, B:G.210, B:S.212, B:S.212, B:A.215, B:D.218 pi-Stacking: B:W.190, B:F.191

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 5 residues within 4Å: Chain A: D.209, D.211, D.236, D.237 Ligands: ZM3.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.209, A:D.236, A:D.237, H2O.14 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.143, D.144 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.143, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: D.209, D.211, D.236, D.237 Ligands: ZM3.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.209, B:D.236, B:D.237, H2O.29 MG.9: 1 residues within 4Å: Chain B: D.145 No protein-ligand interaction detected (PLIP)

2 x ZM3: MYCINAMICIN III(Non-covalent)

ZM3.5: 18 residues within 4Å: Chain A: A.50, G.51, Y.69, R.81, M.152, L.154, Y.157, L.163, D.209, D.211, D.236, D.237, C.239, I.240, P.241, Q.266 Ligands: SAH.1, MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.50, A:L.154, A:Y.157, A:Y.157, A:I.240 Hydrogen bonds: A:Y.69, A:R.81, A:D.211 Water bridges: A:L.52, A:R.81, A:D.209, A:D.236, A:Q.266 ZM3.10: 17 residues within 4Å: Chain B: A.50, G.51, Y.69, R.81, L.154, Y.157, L.163, D.209, D.211, D.236, D.237, C.239, I.240, P.241, Q.266 Ligands: SAH.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.50, B:L.154, B:Y.157, B:Y.157 Hydrogen bonds: B:R.81 Water bridges: B:L.52, B:R.81, B:D.209, B:D.236, B:Q.266

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: H.155, Q.156, Y.157, N.158, A.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.158 Water bridges: A:A.159 DMS.11: 3 residues within 4Å: Chain B: L.93, R.94, Y.122 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.122

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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