SMTL ID : 8jqp.1

Protocatecuate hydroxylase from Xylophilus ampelinus complexed with 3,4-dihydroxybenzoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: V.28, G.29, G.31, P.32, A.33, I.51, E.52, R.53, V.59, R.62, R.64, A.65, G.66, V.67, Q.122, V.146, C.178, D.179, G.180, G.183, V.184, Y.242, T.286, G.305, D.306, P.313, A.316, K.317, G.318, L.319, N.320 Ligands: DHB.2, DHB.3 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:R.64, A:Y.242, A:T.286, A:P.313, A:P.313 Hydrogen bonds: A:G.31, A:A.33, A:R.53, A:R.62, A:R.62, A:R.64, A:A.65, A:G.66, A:V.67, A:V.67, A:Q.122, A:Q.122, A:V.146, A:V.146, A:D.306, A:G.318, A:L.319, A:N.320 Water bridges: A:G.34, A:R.64, A:R.64, A:D.306, A:D.306, A:D.306, A:A.307, A:A.307, A:A.316, A:A.322 Salt bridges: A:R.64 FAD.6: 36 residues within 4Å: Chain B: V.28, G.29, G.31, P.32, A.33, I.51, E.52, R.53, V.59, R.62, R.64, A.65, G.66, V.67, Q.122, P.145, V.146, C.178, D.179, G.180, G.183, V.184, R.240, Y.242, T.286, G.305, D.306, P.313, A.316, K.317, G.318, L.319, N.320, A.322 Ligands: DHB.7, DHB.8 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:R.64, B:R.64, B:Y.242, B:T.286, B:P.313, B:P.313 Hydrogen bonds: B:G.31, B:A.33, B:R.53, B:R.62, B:R.62, B:R.64, B:A.65, B:G.66, B:V.67, B:V.67, B:Q.122, B:Q.122, B:V.146, B:V.146, B:D.306, B:G.318, B:L.319, B:N.320, B:N.320 Water bridges: B:G.34, B:R.64, B:D.306, B:D.306, B:A.307, B:A.307, B:A.316, B:A.322 Salt bridges: B:R.64 pi-Cation interactions: B:R.53

4 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)

DHB.2: 14 residues within 4Å: Chain A: G.66, V.67, V.219, W.221, M.230, S.232, R.234, Y.242, P.313, T.314, G.315, A.316, F.405 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.67, A:A.316 Hydrogen bonds: A:G.66, A:W.221, A:S.232, A:Y.242, A:Y.242 Salt bridges: A:R.234 DHB.3: 6 residues within 4Å: Chain A: R.64, T.286, A.287, D.306, V.311 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.287 Water bridges: A:A.287, A:D.306, A:V.311, A:V.311, A:V.311, A:V.311 DHB.7: 7 residues within 4Å: Chain B: R.64, T.286, A.287, D.306, V.311, P.313 Ligands: FAD.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.287 Water bridges: B:R.64, B:R.64, B:A.287, B:D.306, B:D.306, B:V.311, B:V.311, B:V.311 DHB.8: 12 residues within 4Å: Chain B: G.66, V.67, V.219, W.221, M.230, S.232, Y.242, P.313, T.314, A.316, F.405 Ligands: FAD.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.67, B:A.316 Hydrogen bonds: B:G.66, B:W.221, B:S.232, B:S.232 Water bridges: B:R.240

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.258, S.261, E.262, R.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.261, A:E.262 Water bridges: A:S.261 GOL.9: 4 residues within 4Å: Chain B: R.258, S.261, E.262, R.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.261 Water bridges: B:S.261

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain A: D.257 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.257, A:D.257, H2O.8 CA.10: 2 residues within 4Å: Chain B: D.154, D.155 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.154, B:D.154, H2O.12, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katsuki, N. et al., Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. J.Biol.Chem. (2023)

Release Date

2023-12-06

Peptides

4-hydroxybenzoate 3-monooxygenase (NAD(P)H): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

4-hydroxybenzoate 3-monooxygenase (NAD(P)H)

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