SMTL ID : 3gwz.1 (2 other biounits)

Structure of the Mitomycin 7-O-methyltransferase MmcR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.252 Chain B: D.107 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.107, A:D.252, H2O.3, H2O.6, H2O.19 CA.4: 2 residues within 4Å: Chain B: D.311, R.313 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.311, B:D.311, B:R.313, H2O.18 CA.5: 2 residues within 4Å: Chain B: E.40, D.44 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.40, B:D.44, H2O.11, H2O.13, H2O.16 CA.6: 2 residues within 4Å: Chain B: E.154, D.282 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.154, B:E.154, B:D.282, H2O.11, H2O.17

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: F.165, F.179, M.183, D.280, V.321, L.324, L.325 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.165, A:F.179, A:V.321, A:L.325 Water bridges: A:H.279 MPD.7: 6 residues within 4Å: Chain B: F.179, M.183, D.280, V.321, L.324, L.325 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.321, B:L.324 Water bridges: B:H.279 MPD.9: 6 residues within 4Å: Chain C: F.179, M.183, D.280, V.321, L.324, L.325 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.179, C:V.321, C:L.325 Water bridges: C:H.279 MPD.11: 5 residues within 4Å: Chain D: F.179, D.280, V.321, L.324, L.325 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.179, D:V.321

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

SAH.3: 18 residues within 4Å: Chain A: W.166, F.179, M.183, S.187, G.210, G.211, G.212, E.233, R.234, V.237, G.259, D.260, F.261, F.262, K.275, H.276, D.280, W.281 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.187, A:G.210, A:G.212, A:R.234, A:R.234, A:D.260, A:D.260, A:F.261, A:K.275 Water bridges: A:G.214, A:K.275, A:D.280 Salt bridges: A:K.275 pi-Stacking: A:W.166, A:W.166, A:F.261 SAH.8: 17 residues within 4Å: Chain B: W.166, M.183, S.187, G.210, G.211, G.212, E.233, R.234, V.237, G.259, D.260, F.261, F.262, K.275, H.276, D.280, W.281 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.210, B:G.212, B:R.234, B:R.234, B:D.260, B:F.261, B:K.275 Water bridges: B:K.275 Salt bridges: B:K.275 pi-Stacking: B:W.166, B:W.166, B:F.261 SAH.10: 18 residues within 4Å: Chain C: W.166, F.179, M.183, S.187, G.210, G.211, G.212, L.232, E.233, R.234, V.237, G.259, D.260, F.261, K.275, H.276, D.280, W.281 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.187, C:G.210, C:R.234, C:R.234, C:D.260, C:F.261, C:K.275 Water bridges: C:G.214, C:R.234, C:K.275, C:D.280 Salt bridges: C:K.275 pi-Stacking: C:W.166, C:W.166, C:F.261 SAH.12: 15 residues within 4Å: Chain D: W.166, F.179, M.183, S.187, G.210, G.211, G.212, E.233, R.234, G.259, D.260, F.261, K.275, H.276, D.280 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.187, D:G.210, D:R.234, D:R.234, D:D.260, D:F.261 Water bridges: D:S.187, D:G.214, D:R.234, D:K.275 Salt bridges: D:K.275 pi-Stacking: D:W.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Structural characterization of the mitomycin 7-O-methyltransferase. Proteins (2011)

Release Date

2010-04-07

Peptides

MmcR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

MmcR

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