SMTL ID : 1o94.1

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: V.27, P.28, H.29, C.30, E.59, Y.60, E.103, Y.169, H.172, R.222, W.264, D.267, A.268, V.297, G.298, R.299, C.320, A.321, R.322, P.323, I.352 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:H.29, A:R.322, A:I.352 Hydrogen bonds: A:P.28, A:C.30, A:Y.60, A:E.103, A:Y.169, A:R.222, A:R.222, A:R.299, A:A.321, A:R.322 Water bridges: A:D.267, A:G.298, A:Y.300, A:R.322 Salt bridges: A:R.322 pi-Stacking: A:W.264 pi-Cation interactions: A:H.29 FMN.4: 21 residues within 4Å: Chain B: V.27, P.28, H.29, C.30, E.59, Y.60, E.103, Y.169, H.172, R.222, W.264, D.267, A.268, V.297, R.299, C.320, A.321, R.322, P.323, C.351, I.352 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:H.29, B:R.322, B:I.352 Hydrogen bonds: B:P.28, B:C.30, B:Y.60, B:E.103, B:H.172, B:R.222, B:R.222, B:R.299, B:A.321, B:R.322 Water bridges: B:G.269, B:G.269, B:Y.300 Salt bridges: B:R.322 pi-Stacking: B:W.264 pi-Cation interactions: B:H.29

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: V.395, G.396, G.398, P.399, S.400, D.419, T.420, G.426, H.427, P.469, M.470, A.486, T.487, G.488, A.489, G.673, D.674, A.684 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.398, A:S.400, A:S.400, A:T.420, A:H.427, A:M.470, A:M.470, A:A.489, A:D.674 Water bridges: A:A.397, A:S.400, A:G.401, A:T.420, A:T.420, A:G.426, A:H.427, A:R.644, A:A.675 Salt bridges: A:H.427, A:H.427 ADP.5: 19 residues within 4Å: Chain B: V.395, G.396, G.398, P.399, S.400, D.419, T.420, G.426, H.427, P.469, M.470, A.486, T.487, G.488, A.489, L.650, G.673, D.674, A.684 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.398, B:S.400, B:S.400, B:T.420, B:H.427, B:M.470, B:M.470, B:A.489, B:D.674 Water bridges: B:A.397, B:S.400, B:G.401, B:T.420, B:T.420, B:G.426, B:H.427, B:R.644, B:D.674, B:D.674, B:A.675 Salt bridges: B:H.427, B:H.427

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 13 residues within 4Å: Chain A: R.322, I.325, A.326, C.345, I.346, G.347, C.348, N.349, V.350, C.351, C.364, T.365, Q.366 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.345, A:C.348, A:C.351, A:C.364 SF4.6: 12 residues within 4Å: Chain B: R.322, I.325, A.326, C.345, I.346, G.347, C.348, N.349, V.350, C.351, C.364, T.365 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.345, B:C.348, B:C.351, B:C.364, SF4.6

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 19 residues within 4Å: Chain C: A.6, V.7, K.8, N.36, D.39, V.62, S.63, V.64, V.100, L.104, A.118, G.119, Q.121, S.122, A.126, Y.127, A.128, S.129, T.130 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:N.36, C:D.39, C:V.64, C:V.64, C:G.119, C:S.122, C:Y.127, C:A.128, C:S.129, C:T.130, C:T.130 Water bridges: C:D.39, C:G.131, C:G.131 AMP.8: 19 residues within 4Å: Chain E: A.6, V.7, K.8, N.36, D.39, V.62, S.63, V.64, V.100, L.104, A.118, G.119, Q.121, S.122, A.126, Y.127, A.128, S.129, T.130 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:N.36, E:D.39, E:V.64, E:V.64, E:G.119, E:S.122, E:Y.127, E:A.128, E:S.129, E:T.130, E:T.130 Water bridges: E:S.63, E:G.131, E:G.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leys, D. et al., Extensive Conformational Sampling in a Ternary Electron Transfer Complex. Nat.Struct.Biol. (2003)

Release Date

2003-02-06

Peptides

TRIMETHYLAMINE DEHYDROGENASE: AB
ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT: CE
ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

TRIMETHYLAMINE DEHYDROGENASE

ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT

ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT

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