SMTL ID : 7d4k.1

Crystal structure of Tmm from Pelagibacter sp. strain HTCC7211

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 23 residues within 4Å: Chain A: Y.86, L.89, W.90, N.92, F.182, F.186, P.188, Y.190, G.221, S.222, S.223, Y.224, S.225, D.228, R.246, H.247, C.288, T.289, G.290, Y.291, N.308, R.429 Ligands: FAD.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.86, A:D.228 Hydrogen bonds: A:W.90, A:N.92, A:N.92, A:Y.190, A:S.222, A:S.222, A:S.223, A:S.225, A:S.225, A:N.308, A:R.429 Water bridges: A:N.92, A:G.221, A:S.222, A:S.225, A:A.226, A:R.246, A:R.246, A:R.246, A:R.246, A:R.246, A:R.246, A:H.247, A:C.288, A:Y.291, A:D.334, A:Q.335, A:Q.335 Salt bridges: A:R.246, A:H.247 pi-Cation interactions: A:R.246 NAP.3: 23 residues within 4Å: Chain B: Y.86, L.89, W.90, N.92, F.182, F.186, P.188, Y.190, G.221, S.222, S.223, Y.224, S.225, D.228, R.246, H.247, C.288, T.289, G.290, Y.291, N.308, R.429 Ligands: FAD.4 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:D.228 Hydrogen bonds: B:Y.86, B:W.90, B:N.92, B:N.92, B:Y.190, B:Y.190, B:S.222, B:S.222, B:S.223, B:S.225, B:S.225, B:H.247, B:N.308, B:R.429 Water bridges: B:G.221, B:S.222, B:S.225, B:A.226, B:R.246, B:R.246, B:R.246, B:R.246, B:R.246, B:R.246, B:R.246, B:C.288, B:Y.291, B:Q.335 Salt bridges: B:R.246, B:H.247

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

FAD.2: 32 residues within 4Å: Chain A: I.27, G.28, G.30, P.31, C.32, F.56, E.57, K.58, Q.59, G.64, L.65, W.66, P.82, S.84, M.85, L.89, S.91, N.92, L.98, T.143, R.144, V.145, S.178, T.179, G.180, F.182, F.297, Q.335, T.338, F.339, F.342 Ligands: NAP.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.89, A:F.182 Hydrogen bonds: A:G.30, A:C.32, A:K.58, A:Q.59, A:L.65, A:W.66, A:N.92, A:V.145, A:V.145, A:T.338 Water bridges: A:G.33, A:K.58, A:K.58, A:G.64, A:G.180, A:G.180, A:F.182, A:S.183, A:S.183, A:T.338 pi-Stacking: A:W.66 FAD.4: 31 residues within 4Å: Chain B: I.27, G.28, G.30, P.31, C.32, F.56, E.57, K.58, Q.59, G.64, L.65, W.66, P.82, S.84, M.85, S.91, N.92, L.98, T.143, R.144, V.145, S.178, T.179, G.180, F.182, F.297, Q.335, T.338, F.339, F.342 Ligands: NAP.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.182 Hydrogen bonds: B:G.30, B:C.32, B:K.58, B:Q.59, B:L.65, B:W.66, B:N.92, B:V.145, B:V.145 Water bridges: B:G.33, B:K.58, B:G.64, B:S.91, B:G.93, B:G.180, B:G.180, B:F.182, B:S.183, B:S.183, B:T.338 pi-Stacking: B:W.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X.J. et al., Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation. Front Microbiol (2021)

Release Date

2021-09-15

Peptides

Flavin-containing monooxygenase FMO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavin-containing monooxygenase FMO

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