SMTL ID : 2dki.1

Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, under pressure of xenon gas (12 atm)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.4, A:L.5 Water bridges: A:Q.2, A:N.6, A:N.6, A:N.6, A:N.6, A:R.9 Salt bridges: A:R.9 SO4.2: 4 residues within 4Å: Chain A: E.86, V.487, Q.488, H.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.488 Water bridges: A:K.485, A:K.485 Salt bridges: A:H.491 SO4.3: 5 residues within 4Å: Chain A: G.456, Q.457, A.458, K.459, H.460 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.457, A:A.458, A:K.459, A:H.460 Water bridges: A:H.460 Salt bridges: A:K.459 SO4.8: 4 residues within 4Å: Chain B: F.3, H.4, L.5, R.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.4, B:L.5 Water bridges: B:Q.2, B:N.6, B:N.6, B:N.6, B:N.6, B:R.9 Salt bridges: B:R.9 SO4.9: 4 residues within 4Å: Chain B: E.86, V.487, Q.488, H.491 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.488 Water bridges: B:K.485, B:K.485 Salt bridges: B:H.491 SO4.10: 5 residues within 4Å: Chain B: G.456, Q.457, A.458, K.459, H.460 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.457, B:A.458, B:K.459, B:H.460 Water bridges: 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, A.74, 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 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Q.73, A:Q.73 Hydrogen bonds: A:A.43, A:Q.64, A:Q.64, 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:Q.73, A:Q.140, A:G.208, A:A.209, A:A.350, A:M.362 pi-Stacking: A:Y.317, A:Y.317 FAD.11: 26 residues within 4Å: Chain B: V.38, G.39, G.41, P.42, A.43, E.63, Q.64, K.65, Q.73, A.74, 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 B Hydrophobic interactions: B:Q.73, B:Q.73 Hydrogen bonds: B:A.43, B:Q.64, B:Q.64, 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:Q.73, B:Q.140, B:G.208, B:A.209, B:A.350, B:M.362 pi-Stacking: B:Y.317, B:Y.317

6 x XE: XENON(Non-covalent)

XE.5: 3 residues within 4Å: Chain A: W.230, L.258, P.356 No protein-ligand interaction detected (PLIP) XE.6: 5 residues within 4Å: Chain A: L.501, L.524, P.531, L.532, F.546 No protein-ligand interaction detected (PLIP) XE.7: 2 residues within 4Å: Chain A: A.631, S.635 No protein-ligand interaction detected (PLIP) XE.12: 3 residues within 4Å: Chain B: W.230, L.258, P.356 No protein-ligand interaction detected (PLIP) XE.13: 5 residues within 4Å: Chain B: L.501, L.524, P.531, L.532, F.546 No protein-ligand interaction detected (PLIP) XE.14: 2 residues within 4Å: Chain B: A.631, S.635 No protein-ligand interaction detected (PLIP)

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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