SMTL ID : 3nvc.1

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with salicylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.119, H.121, H.160 Ligands: SAL.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.121, A:H.160 FE2.6: 4 residues within 4Å: Chain B: H.119, H.121, H.160 Ligands: SAL.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.121, B:H.160 FE2.11: 4 residues within 4Å: Chain C: H.119, H.121, H.160 Ligands: SAL.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.121, C:H.160 FE2.16: 4 residues within 4Å: Chain D: H.119, H.121, H.160 Ligands: SAL.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.121, D:H.160

4 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.2: 9 residues within 4Å: Chain A: Q.108, H.119, H.121, R.127, H.160, D.174 Chain B: L.38, M.46 Ligands: FE2.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Water bridges: A:R.127, A:R.127, A:R.127, A:W.172 Salt bridges: A:H.119, A:H.121, A:R.127, A:H.160 Hydrophobic interactions: B:L.38 SAL.7: 9 residues within 4Å: Chain A: L.38, M.46 Chain B: Q.108, H.119, H.121, R.127, H.160, D.174 Ligands: FE2.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Water bridges: B:R.127, B:R.127, B:R.127, B:W.172 Salt bridges: B:H.119, B:H.121, B:R.127, B:H.160 Hydrophobic interactions: A:L.38 SAL.12: 9 residues within 4Å: Chain C: Q.108, H.119, H.121, R.127, H.160, D.174 Chain D: L.38, M.46 Ligands: FE2.11 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Water bridges: C:R.127, C:T.154, C:T.154, C:W.172, C:D.174, C:D.174 Salt bridges: C:H.119, C:H.121, C:R.127, C:H.160 Hydrophobic interactions: D:L.38 SAL.17: 9 residues within 4Å: Chain C: L.38, M.46 Chain D: Q.108, H.119, H.121, R.127, H.160, D.174 Ligands: FE2.16 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Water bridges: D:R.127, D:T.154, D:T.154, D:W.172, D:D.174, D:D.174 Salt bridges: D:H.119, D:H.121, D:R.127, D:H.160 Hydrophobic interactions: C:L.38

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.265, E.282, R.295, E.297, R.347 Chain C: L.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.265, A:E.282, A:E.297, A:R.347, A:R.347 Water bridges: A:R.295 GOL.4: 7 residues within 4Å: Chain A: L.38, Q.41, L.42, G.43, L.45 Chain B: R.83 Ligands: GOL.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.41, A:L.45, B:R.83 GOL.5: 6 residues within 4Å: Chain A: G.43, M.46, I.48 Chain B: F.189, F.191 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain B: R.265, E.282, R.295, E.297, R.347 Chain D: L.219 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.265, B:E.282, B:E.297, B:R.347, B:R.347 Water bridges: B:R.295 GOL.9: 7 residues within 4Å: Chain A: R.83 Chain B: L.38, Q.41, L.42, G.43, L.45 Ligands: GOL.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.41, B:L.45, A:R.83 GOL.10: 6 residues within 4Å: Chain A: F.189, F.191 Chain B: G.43, M.46, I.48 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) GOL.13: 6 residues within 4Å: Chain A: L.219 Chain C: R.265, E.282, R.295, E.297, R.347 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.265, C:E.282, C:E.297, C:R.347, C:R.347 Water bridges: C:R.295 GOL.14: 7 residues within 4Å: Chain C: L.38, Q.41, L.42, G.43, L.45 Chain D: R.83 Ligands: GOL.15 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.83, C:Q.41, C:L.45 GOL.15: 6 residues within 4Å: Chain C: G.43, M.46, I.48 Chain D: F.189, F.191 Ligands: GOL.14 No protein-ligand interaction detected (PLIP) GOL.18: 6 residues within 4Å: Chain B: L.219 Chain D: R.265, E.282, R.295, E.297, R.347 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.265, D:E.282, D:E.297, D:R.347, D:R.347 Water bridges: D:R.295 GOL.19: 7 residues within 4Å: Chain C: R.83 Chain D: L.38, Q.41, L.42, G.43, L.45 Ligands: GOL.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.41, D:L.45, C:R.83 GOL.20: 6 residues within 4Å: Chain C: F.189, F.191 Chain D: G.43, M.46, I.48 Ligands: GOL.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate. FEBS J. (2013)

Release Date

2011-07-13

Peptides

Gentisate 1,2-Dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Gentisate 1,2-Dioxygenase

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