SMTL ID : 3ssn.1

MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway in Complex with Mg, SAH, and Mycinamycin VI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.295, H.298, E.323, D.324 Ligands: MVI.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.295, A:D.324, H2O.5, H2O.5 MG.6: 4 residues within 4Å: Chain C: D.295, E.323, D.324 Ligands: MVI.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.295, C:D.324, H2O.16, H2O.16 MG.10: 3 residues within 4Å: Chain D: D.295, E.323, D.324 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.295, D:D.324

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

SAH.2: 21 residues within 4Å: Chain A: T.193, P.194, K.195, E.222, G.224, V.225, G.226, G.227, Y.228, S.237, D.254, I.255, M.256, G.271, D.272, Q.273, D.295, G.296, S.297, H.302 Chain D: F.407 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.195, A:G.226, A:G.226, A:Y.228, A:S.237, A:S.237, A:I.255, A:D.272, A:Q.273, A:D.295, A:D.295, A:H.302 Water bridges: A:V.225, A:V.225, A:G.236, A:S.237 Salt bridges: A:K.195 SAH.7: 21 residues within 4Å: Chain B: F.407 Chain C: T.193, P.194, K.195, E.222, G.224, V.225, G.226, G.227, Y.228, S.237, D.254, I.255, M.256, G.271, D.272, Q.273, D.295, G.296, S.297, H.302 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.195, C:G.226, C:G.226, C:Y.228, C:S.237, C:S.237, C:I.255, C:D.272, C:Q.273, C:D.295, C:H.302 Water bridges: C:G.235 Salt bridges: C:K.195 SAH.11: 20 residues within 4Å: Chain A: F.407 Chain D: T.193, K.195, E.222, G.224, V.225, G.226, G.227, Y.228, S.237, D.254, I.255, M.256, G.271, D.272, Q.273, D.295, G.296, S.297, H.302 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.193, D:G.224, D:V.225, D:V.225, D:G.226, D:G.226, D:Y.228, D:S.237, D:S.237, D:I.255, D:K.258, D:D.272, D:D.272, D:Q.273 Salt bridges: D:K.195

2 x MVI: Mycinamicin VI(Non-covalent)

MVI.3: 20 residues within 4Å: Chain A: F.192, T.193, P.194, L.199, H.200, Y.228, W.233, D.295, H.298, D.324, W.326 Chain C: I.159, G.160, L.164, Q.167 Chain D: I.403, L.410, A.413, S.414 Ligands: MG.1 12 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:F.192, A:P.194, A:L.199, A:W.233, D:I.403, D:I.403, C:I.159 Hydrogen bonds: A:H.200, A:D.295, A:W.326 Water bridges: C:G.160, C:L.164 MVI.8: 18 residues within 4Å: Chain A: G.160, L.163, L.164, Q.167 Chain B: I.403, L.410, A.413, S.414 Chain C: F.192, P.194, H.200, Y.228, W.233, D.295, H.298, D.324, W.326 Ligands: MG.6 9 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:P.194, C:W.233, A:L.163, B:I.403, B:I.403 Hydrogen bonds: C:H.200, C:D.324, C:W.326 Water bridges: A:G.160

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

DMS.4: 6 residues within 4Å: Chain A: R.208, H.209, H.381 Chain D: R.208, H.209, Y.383 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.208 Water bridges: A:Y.383, D:H.209 DMS.5: 7 residues within 4Å: Chain A: R.69, A.175, G.178, S.179, R.180, P.182, S.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69 DMS.9: 7 residues within 4Å: Chain C: R.69, A.175, G.178, S.179, R.180, P.182, S.243 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.69

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain D: R.97, R.105, V.107, E.111 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.105, D:E.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akey, D.L. et al., A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway. J.Mol.Biol. (2011)

Release Date

2011-08-24

Peptides

Methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methyltransferase

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