SMTL ID : 2dkh.1

Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: F.3, H.4, L.5, R.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.4, A:L.5, A:N.6 Water bridges: A:Q.2, A:N.6, A:N.6, A:P.13 Salt bridges: A:R.9 SO4.2: 4 residues within 4Å: Chain A: E.86, V.487, Q.488, H.491 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.96, A:H.491 Hydrogen bonds: A:Q.488 Water bridges: A:K.485 SO4.3: 4 residues within 4Å: Chain A: G.456, Q.457, A.458, K.459 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.457, A:A.458, A:K.459 Water bridges: A:A.458, A:K.459, A:K.459, A:H.460, A:H.460, A:V.620 Salt bridges: A:K.459 SO4.6: 4 residues within 4Å: Chain B: F.3, H.4, L.5, R.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.4, B:L.5, B:N.6 Water bridges: B:Q.2, B:N.6, B:N.6, B:P.13 Salt bridges: B:R.9 SO4.7: 4 residues within 4Å: Chain B: E.86, V.487, Q.488, H.491 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.488 Water bridges: B:K.485 Salt bridges: B:H.491, A:K.96 SO4.8: 4 residues within 4Å: Chain B: G.456, Q.457, A.458, K.459 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.457, B:A.458, B:K.459 Water bridges: B:A.458, B:K.459, B:H.460, B:H.460, B:H.460, B:H.460 Salt bridges: B:K.459

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

FAD.4: 26 residues within 4Å: Chain A: V.38, G.39, G.41, P.42, A.43, E.63, Q.64, K.65, Q.73, Q.140, R.164, R.165, V.166, C.206, D.207, G.208, N.212, V.232, R.269, Y.271, S.315, Y.317, G.348, D.349, G.361, S.365 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Q.73 Hydrogen bonds: A:A.43, A:Q.64, A:Q.64, A:Q.140, A:V.166, A:V.166, A:N.212, A:R.269, A:Y.271, A:Y.271, A:D.349, A:S.365, A:S.365 Water bridges: A:C.40, A:G.41, A:G.44, A:D.75, A:G.208, A:N.212, A:N.212, A:A.350 pi-Stacking: A:Y.317, A:Y.317 FAD.9: 26 residues within 4Å: Chain B: V.38, G.39, G.41, P.42, A.43, E.63, Q.64, K.65, Q.73, Q.140, R.164, R.165, V.166, C.206, D.207, G.208, N.212, V.232, R.269, Y.271, S.315, Y.317, G.348, D.349, G.361, S.365 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Q.73 Hydrogen bonds: B:A.43, B:Q.64, B:Q.64, B:Q.140, B:V.166, B:V.166, B:N.212, B:R.269, B:Y.271, B:D.349, B:S.365, B:S.365 Water bridges: B:C.40, B:G.41, B:G.44, B:D.75, B:G.208, B:N.212, B:N.212, B:A.350 pi-Stacking: B:Y.317, B:Y.317

2 x 3HB: 3-HYDROXYBENZOIC ACID(Non-covalent)

3HB.5: 8 residues within 4Å: Chain A: D.75, G.76, H.135, I.137, K.247, L.258, I.260, Y.271 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.258, A:I.260, A:Y.271 Hydrogen bonds: A:D.75 Water bridges: A:D.75, A:H.135, A:K.247 Salt bridges: A:H.135, A:K.247 3HB.10: 8 residues within 4Å: Chain B: D.75, G.76, H.135, I.137, K.247, L.258, I.260, Y.271 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.258, B:I.260, B:Y.271 Hydrogen bonds: B:D.75, B:Y.271 Water bridges: B:D.75, B:K.247, B:K.247 Salt bridges: B:H.135, B:K.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiromoto, T. et al., Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site. J.Mol.Biol. (2006)

Release Date

2006-10-24

Peptides

3-hydroxybenzoate hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-hydroxybenzoate hydroxylase

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