SMTL ID : 3nkt.1

Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with naphthoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 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: 1HN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.121, A:H.160 FE2.5: 4 residues within 4Å: Chain B: H.119, H.121, H.160 Ligands: 1HN.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.121, B:H.160 FE2.9: 4 residues within 4Å: Chain C: H.119, H.121, H.160 Ligands: 1HN.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.121, C:H.160 FE2.13: 4 residues within 4Å: Chain D: H.119, H.121, H.160 Ligands: 1HN.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.121, D:H.160

4 x 1HN: 1-hydroxynaphthalene-2-carboxylic acid(Non-covalent)

1HN.2: 14 residues within 4Å: Chain A: R.83, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain B: L.38, M.46 Ligands: FE2.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.83, A:D.174, A:L.176, A:L.176, A:I.178, B:L.38, B:L.38 Salt bridges: A:R.83, A:H.119, A:R.127, A:H.160, A:H.162 pi-Stacking: A:W.104, A:W.104 1HN.6: 14 residues within 4Å: Chain A: L.38, M.46 Chain B: R.83, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE2.5 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.83, B:D.174, B:L.176, B:L.176, B:I.178, A:L.38, A:L.38 Salt bridges: B:R.83, B:H.119, B:R.127, B:H.160, B:H.162 pi-Stacking: B:W.104, B:W.104 1HN.10: 14 residues within 4Å: Chain C: R.83, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain D: L.38, M.46 Ligands: FE2.9 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:R.83, C:D.174, C:L.176, C:L.176, C:I.178, D:L.38, D:L.38 Salt bridges: C:R.83, C:H.119, C:R.127, C:H.160, C:H.162 pi-Stacking: C:W.104, C:W.104 1HN.14: 14 residues within 4Å: Chain C: L.38, M.46 Chain D: R.83, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE2.13 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:R.83, D:D.174, D:L.176, D:L.176, D:I.178, C:L.38, C:L.38 Salt bridges: D:R.83, D:H.119, D:R.127, D:H.160, D:H.162 pi-Stacking: D:W.104, D:W.104

8 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.265, A:E.282, A:E.297, A:R.347, A:R.347 GOL.4: 6 residues within 4Å: Chain A: F.204, E.208, C.212, H.213, F.237 Chain C: E.244 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.244, C:E.244 Water bridges: A:H.213 GOL.7: 6 residues within 4Å: Chain B: R.265, E.282, R.295, E.297, R.347 Chain D: L.219 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.265, B:E.282, B:E.297, B:R.347, B:R.347 GOL.8: 6 residues within 4Å: Chain B: F.204, E.208, C.212, H.213, F.237 Chain D: E.244 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.244, D:E.244 Water bridges: B:H.213 GOL.11: 6 residues within 4Å: Chain A: L.219 Chain C: R.265, E.282, R.295, E.297, R.347 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.265, C:E.282, C:E.297, C:R.347, C:R.347 GOL.12: 6 residues within 4Å: Chain A: E.244 Chain C: F.204, E.208, C.212, H.213, F.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.244 GOL.15: 6 residues within 4Å: Chain B: L.219 Chain D: R.265, E.282, R.295, E.297, R.347 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.265, D:E.282, D:E.297, D:R.347, D:R.347 GOL.16: 6 residues within 4Å: Chain B: E.244 Chain D: F.204, E.208, C.212, H.213, F.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases. J.Struct.Biol. (2012)

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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