SMTL ID : 5g3t.1 (1 other biounit)

The structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.1: 41 residues within 4Å: Chain A: V.15, G.16, A.17, G.18, I.19, S.20, G.21, F.42, D.43, M.44, Q.45, G.49, G.50, R.51, I.52, L.65, G.66, A.67, G.68, R.69, Y.70, Y.211, R.212, L.213, A.245, I.246, P.247, A.250, L.254, L.272, K.274, Y.314, W.364, G.367, S.393, D.394, G.401, W.402, M.403, E.404 Ligands: MG.2 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:R.51, A:L.272, A:W.364 Hydrogen bonds: A:G.18, A:S.20, A:S.20, A:S.20, A:M.44, A:G.50, A:R.51, A:A.67, A:G.68, A:R.69, A:R.69, A:R.69, A:L.213, A:L.213, A:D.394, A:D.394, A:W.402, A:M.403 Water bridges: A:I.19, A:D.43, A:D.43, A:Q.45, A:R.51, A:R.51, A:I.52, A:G.66, A:R.69, A:R.212, A:R.212, A:R.212, A:R.212, A:R.212, A:Y.314, A:S.393, A:S.393, A:E.404 Salt bridges: A:R.51, A:R.51 FDA.5: 42 residues within 4Å: Chain B: V.15, G.16, A.17, G.18, I.19, S.20, G.21, F.42, D.43, M.44, Q.45, G.49, G.50, R.51, I.52, L.65, G.66, A.67, G.68, R.69, Y.70, Y.211, R.212, L.213, A.245, I.246, P.247, A.250, L.254, L.272, K.274, Y.314, W.364, G.367, S.393, D.394, G.401, W.402, M.403, E.404 Ligands: MG.7, TRS.10 37 PLIP interactions: 37 interactions with chain B Hydrophobic interactions: B:R.51, B:L.272, B:W.364 Hydrogen bonds: B:G.18, B:S.20, B:S.20, B:S.20, B:M.44, B:G.50, B:R.51, B:R.51, B:A.67, B:G.68, B:R.69, B:R.69, B:R.69, B:L.213, B:L.213, B:D.394, B:W.402, B:M.403 Water bridges: B:I.19, B:D.43, B:D.43, B:Q.45, B:R.51, B:I.52, B:G.66, B:R.212, B:R.212, B:R.212, B:S.393, B:S.393, B:S.393, B:E.404 Salt bridges: B:R.51, B:R.51

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: G.16, A.17, G.18, S.20, G.21, A.245 Ligands: FDA.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.245, FDA.1 MG.6: 5 residues within 4Å: Chain B: K.108, M.111, N.112, V.174, T.175 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.108, B:V.174, H2O.19, H2O.19 MG.7: 7 residues within 4Å: Chain B: G.16, A.17, G.18, S.20, G.21, A.245 Ligands: FDA.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.245, FDA.5

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: R.51, W.364, A.365, H.366, G.367 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: E.47, A.48, Q.194, K.197, L.209 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: S.101, H.102 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: R.51, W.364, A.365, H.366, G.367 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 10 residues within 4Å: Chain B: R.69, Y.148, H.168, L.272, Y.314, G.367, V.368, G.401, W.402 Ligands: FDA.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.69, B:R.69, B:Y.314, B:G.401 Water bridges: B:G.367, B:G.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuller, J. et al., Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum. J.Biol.Chem. (2016)

Release Date

2016-08-03

Peptides

L-TRYPTOPHAN OXIDASE VIOA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-TRYPTOPHAN OXIDASE VIOA

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