SMTL ID : 3o5u.1

Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with protocatechuate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: Y.134, R.191, H.194, H.196 Ligands: DHB.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.134, A:H.194, A:H.196 FE.10: 4 residues within 4Å: Chain B: Y.134, H.194, H.196 Ligands: DHB.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.134, B:H.194, B:H.196

2 x MYY: (2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE(Non-covalent)

MYY.2: 14 residues within 4Å: Chain A: F.20, I.21, E.30, T.33, I.34, Y.37, M.38, W.50, Y.184 Chain B: V.6, F.10, F.13, M.38 Ligands: MYY.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.20, A:I.21, A:E.30, A:I.34, A:W.50, A:Y.184, B:F.13, B:F.13 MYY.3: 12 residues within 4Å: Chain A: N.3, V.6, L.9, F.13, M.38 Chain B: F.20, T.33, I.34, Y.37, W.50, Y.184 Ligands: MYY.2 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.20, B:I.34, B:Y.37, B:Y.37, B:W.50, B:W.50, B:Y.184, A:V.6, A:L.9, A:F.13, A:F.13, A:F.13, A:F.13 Hydrogen bonds: A:N.3

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

DHB.4: 15 residues within 4Å: Chain A: L.49, D.52, A.53, I.74, G.76, P.77, F.78, Y.134, Y.169, I.171, R.191, H.194, H.196, C.224 Ligands: FE.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.49, A:Y.169, A:I.171, A:R.191 Hydrogen bonds: A:A.53, A:R.191 pi-Stacking: A:F.78 pi-Cation interactions: A:R.191 DHB.11: 15 residues within 4Å: Chain B: L.49, D.52, A.53, I.74, G.76, P.77, F.78, Y.134, Y.169, I.171, R.191, H.194, H.196, C.224 Ligands: FE.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.169, B:I.171 Hydrogen bonds: B:R.191 pi-Stacking: B:F.78 pi-Cation interactions: B:R.191

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.52, E.56, Q.75, G.76, P.77 Chain B: E.32, M.35 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.32, B:E.32, A:Q.75 GOL.6: 2 residues within 4Å: Chain A: K.228, S.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.229 Water bridges: A:E.230 GOL.12: 6 residues within 4Å: Chain A: E.32, M.35 Chain B: D.52, E.56, Q.75, G.76 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.32, B:D.52, B:E.56

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: T.113, H.256 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: E.81 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: D.202, G.203 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: G.203, N.257 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity. J. Struct. Biol. (2013)

Release Date

2011-08-17

Peptides

Chlorocatechol 1,2-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chlorocatechol 1,2-dioxygenase

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