SMTL ID : 5gsn.1 (1 other biounit)

Tmm in complex with methimazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: N.73, F.165, N.169, P.171, Y.173, M.203, G.204, A.205, S.206, S.207, S.208, R.229, S.230, C.271, T.272, G.273, Y.274, N.291, D.317, Q.318, W.319, W.401 Ligands: MMZ.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.319, A:W.401 Hydrogen bonds: A:N.169, A:Y.173, A:A.205, A:S.206, A:S.207, A:S.208, A:R.229, A:S.230, A:N.291, A:D.317, A:Q.318, A:Q.318 Water bridges: A:N.73, A:N.73, A:Y.173, A:S.206, A:S.206, A:S.208, A:C.271, A:Y.274, A:Y.274 Salt bridges: A:R.229 pi-Cation interactions: A:R.229, A:R.229 NAP.4: 23 residues within 4Å: Chain B: N.73, F.165, N.169, P.171, Y.173, M.203, G.204, A.205, S.206, S.207, S.208, R.229, S.230, C.271, T.272, G.273, Y.274, N.291, D.317, Q.318, T.321 Ligands: FAD.5, MMZ.6 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:N.73, B:N.169, B:A.205, B:S.206, B:S.207, B:S.208, B:S.208, B:R.229, B:S.230, B:N.291, B:D.317, B:Q.318 Water bridges: B:N.169, B:Y.173, B:S.206, B:S.208, B:A.209, B:S.230, B:S.230, B:G.273 Salt bridges: B:R.229 pi-Cation interactions: B:R.229, B:R.229

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 30 residues within 4Å: Chain A: I.8, G.9, G.11, P.12, S.13, F.37, E.38, K.39, Q.40, G.45, L.46, W.47, H.63, S.65, M.66, S.72, N.73, L.79, P.125, V.126, A.161, S.162, G.163, F.165, F.280, Q.318, T.321, F.322, F.325 Ligands: MMZ.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.46, A:F.165 Hydrogen bonds: A:G.11, A:S.13, A:S.13, A:K.39, A:Q.40, A:L.46, A:W.47, A:N.73, A:V.126, A:V.126, A:Q.318 Water bridges: A:S.13, A:G.14, A:N.73, A:G.74, A:G.163, A:H.164, A:H.164, A:T.321 Salt bridges: A:H.63 pi-Stacking: A:W.47 pi-Cation interactions: A:K.39 FAD.5: 31 residues within 4Å: Chain B: I.8, G.9, G.11, P.12, S.13, F.37, E.38, K.39, Q.40, G.45, L.46, W.47, H.63, S.65, S.72, N.73, L.79, S.124, P.125, V.126, A.161, S.162, G.163, F.165, F.280, Q.318, T.321, F.322, F.325 Ligands: NAP.4, MMZ.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.46, B:F.165 Hydrogen bonds: B:G.11, B:S.13, B:S.13, B:K.39, B:Q.40, B:G.45, B:L.46, B:W.47, B:N.73, B:V.126, B:V.126, B:T.321 Water bridges: B:G.14, B:K.39, B:G.74, B:G.74, B:G.163, B:H.164, B:Q.318, B:R.413 Salt bridges: B:H.63 pi-Stacking: B:W.47 pi-Cation interactions: B:K.39

2 x MMZ: 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE(Non-covalent)

MMZ.3: 5 residues within 4Å: Chain A: N.73, S.207, S.208 Ligands: NAP.1, FAD.2 No protein-ligand interaction detected (PLIP) MMZ.6: 6 residues within 4Å: Chain B: Y.67, N.73, S.207, S.208 Ligands: NAP.4, FAD.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C.Y. et al., Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide. Mol. Microbiol. (2017)

Release Date

2017-01-18

Peptides

Flavin-containing monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Flavin-containing monooxygenase

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