SMTL ID : 6ju1.1

p-Hydroxybenzoate hydroxylase Y385F mutant complexed with 3,4-dihydroxybenzoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: I.28, G.29, G.31, P.32, S.33, L.51, E.52, R.53, Q.54, V.59, R.62, R.64, A.65, G.66, V.67, Q.122, V.147, C.178, D.179, G.180, G.183, I.184, Y.242, G.305, D.306, P.313, A.316, K.317, G.318, L.319, N.320 Ligands: DHB.2, BR.9 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:P.313, A:P.313 Hydrogen bonds: A:G.31, A:S.33, A:S.33, A:S.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:I.184, A:D.306, A:G.318, A:L.319, A:N.320 Water bridges: A:G.34, A:R.53, A:R.53, A:R.62, A:V.147, A:G.180, A:F.181, A:D.306, A:D.306, A:D.306, A:D.306, A:A.307, A:A.322 Salt bridges: A:R.62, A:R.64 FAD.11: 33 residues within 4Å: Chain B: I.28, G.29, G.31, P.32, S.33, L.51, E.52, R.53, Q.54, V.59, R.62, R.64, A.65, G.66, V.67, Q.122, V.147, C.178, D.179, G.180, G.183, I.184, Y.242, G.305, D.306, P.313, A.316, K.317, G.318, L.319, N.320 Ligands: DHB.12, BR.19 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:P.313, B:P.313 Hydrogen bonds: B:G.31, B:S.33, B:S.33, B:S.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:I.184, B:D.306, B:G.318, B:L.319, B:N.320 Water bridges: B:G.34, B:R.53, B:R.53, B:R.62, B:V.147, B:G.180, B:F.181, B:D.306, B:D.306, B:D.306, B:D.306, B:A.307, B:A.322 Salt bridges: B:R.62, B:R.64

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

DHB.2: 15 residues within 4Å: Chain A: R.64, G.66, V.67, W.205, L.219, Y.221, L.230, S.232, R.234, R.240, Y.242, P.313, T.314, A.316 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.67, A:W.205, A:L.219, A:L.230, A:Y.242 Hydrogen bonds: A:G.66, A:Y.221, A:S.232, A:Y.242, A:Y.242 Water bridges: A:R.234 Salt bridges: A:R.234 DHB.12: 15 residues within 4Å: Chain B: R.64, G.66, V.67, W.205, L.219, Y.221, L.230, S.232, R.234, R.240, Y.242, P.313, T.314, A.316 Ligands: FAD.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.67, B:W.205, B:L.219, B:L.230, B:Y.242 Hydrogen bonds: B:G.66, B:Y.221, B:Y.221, B:S.232, B:Y.242 Water bridges: B:Y.242 Salt bridges: B:R.234

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Q.187, I.189, P.190, A.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.187, A:A.191 GOL.4: 4 residues within 4Å: Chain A: R.186, Q.187, E.198, F.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.186, A:Q.187, A:E.198 Water bridges: A:F.181, A:E.198 GOL.5: 8 residues within 4Å: Chain A: R.361, F.362, W.365, Y.391, T.400, I.401, N.404 Chain B: Y.391 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.361, A:R.361, B:E.387 GOL.6: 9 residues within 4Å: Chain A: E.69, Q.70, G.71, K.115, R.355, V.406, G.407, L.408, Y.410 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.69, A:Q.70, A:G.71, A:K.115, A:K.115, A:R.355, A:V.406, A:Y.410, A:Y.410 Water bridges: A:R.355 GOL.13: 4 residues within 4Å: Chain B: Q.187, I.189, P.190, A.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.187, B:A.191 GOL.14: 4 residues within 4Å: Chain B: R.186, Q.187, E.198, F.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.186, B:Q.187, B:E.198 Water bridges: B:F.181 GOL.15: 8 residues within 4Å: Chain A: Y.391 Chain B: R.361, F.362, W.365, Y.391, T.400, I.401, N.404 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.361, B:R.361, B:T.400, A:E.387, A:Y.391 GOL.16: 9 residues within 4Å: Chain B: E.69, Q.70, G.71, K.115, R.355, V.406, G.407, L.408, Y.410 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.70, B:G.71, B:K.115, B:K.115, B:R.355, B:V.406, B:Y.410 Water bridges: B:R.355

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 11 residues within 4Å: Chain A: R.110, L.111, E.395, A.396, A.399 Chain B: R.110, L.111, E.395, A.396, A.399 Ligands: PG4.17 No protein-ligand interaction detected (PLIP) PG4.17: 11 residues within 4Å: Chain A: R.110, L.111, E.395, A.396, A.399 Chain B: R.110, L.111, E.395, A.396, A.399 Ligands: PG4.7 No protein-ligand interaction detected (PLIP)

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.8: 15 residues within 4Å: Chain A: W.364, W.365, S.368, V.369, F.373, S.380, Q.384, E.387 Chain B: W.364, W.365, S.368, V.369, F.373, E.387 Ligands: P33.18 No protein-ligand interaction detected (PLIP) P33.18: 15 residues within 4Å: Chain A: W.364, W.365, S.368, V.369, F.373, E.387 Chain B: W.364, W.365, S.368, V.369, F.373, S.380, Q.384, E.387 Ligands: P33.8 No protein-ligand interaction detected (PLIP)

4 x BR: BROMIDE ION(Non-covalent)

BR.9: 6 residues within 4Å: Chain A: V.311, P.313, A.316, K.317, G.318 Ligands: FAD.1 Ligand excluded by PLIP BR.10: 6 residues within 4Å: Chain A: I.63, A.65, G.121, Q.122, T.123, R.234 Ligand excluded by PLIP BR.19: 6 residues within 4Å: Chain B: V.311, P.313, A.316, K.317, G.318 Ligands: FAD.11 Ligand excluded by PLIP BR.20: 6 residues within 4Å: Chain B: I.63, A.65, G.121, Q.122, T.123, R.234 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moriwaki, Y. et al., Understanding the Molecular Mechanism Underlying the High Catalytic Activity ofp-Hydroxybenzoate Hydroxylase Mutants for Producing Gallic Acid. Biochemistry (2019)

Release Date

2019-11-06

Peptides

4-hydroxybenzoate 3-monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxybenzoate 3-monooxygenase