SMTL ID : 3hgi.1

Crystal structure of Catechol 1,2-Dioxygenase from the gram-positive Rhodococcus opacus 1CP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: Y.162, Y.196, H.220, H.222 Ligands: CO3.2, BEZ.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:Y.162, A:Y.196, A:H.220, A:H.222 FE.5: 6 residues within 4Å: Chain B: Y.162, Y.196, H.220, H.222 Ligands: CO3.6, BEZ.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.162, B:Y.196, B:H.220, B:H.222

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.2: 7 residues within 4Å: Chain A: H.155, A.156, Y.162, Y.196, H.220, H.222 Ligands: FE.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.156 Water bridges: A:A.156, A:H.220, A:H.220 CO3.6: 7 residues within 4Å: Chain B: H.155, A.156, Y.162, Y.196, H.220, H.222 Ligands: FE.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.156 Water bridges: B:A.156, B:H.220, B:H.220

2 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.3: 17 residues within 4Å: Chain A: A.25, T.26, A.27, T.29, L.34, I.37, L.45 Chain B: L.45, I.49, E.58, V.61, F.62, W.65, L.79, Q.206, F.207, A.210 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.49, B:E.58, B:V.61, B:F.62, B:F.62, B:W.65, B:W.65, B:L.79, B:Q.206, B:F.207, B:F.207, A:L.34, A:I.37, A:L.45 Hydrogen bonds: A:A.27, A:T.29 Water bridges: A:R.24, A:R.24 Salt bridges: A:R.24 6PL.7: 17 residues within 4Å: Chain A: L.45, I.49, E.58, V.61, F.62, W.65, L.79, Q.206, F.207, A.210 Chain B: A.25, T.26, A.27, T.29, L.34, I.37, L.45 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.34, B:I.37, B:L.45, A:I.49, A:E.58, A:V.61, A:F.62, A:F.62, A:W.65, A:W.65, A:L.79, A:Q.206, A:F.207, A:F.207 Hydrogen bonds: B:A.27, B:T.29 Water bridges: B:R.24, B:R.24 Salt bridges: B:R.24

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.4: 13 residues within 4Å: Chain A: L.77, D.80, V.81, I.102, G.104, P.105, Y.106, Y.162, Y.196, R.217, H.220, H.222 Ligands: FE.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.77, A:D.80, A:V.81, A:I.102, A:Y.106 Hydrogen bonds: A:Q.236 Salt bridges: A:R.217, A:H.220, A:H.222 BEZ.8: 13 residues within 4Å: Chain B: L.77, D.80, V.81, I.102, G.104, P.105, Y.106, Y.162, Y.196, R.217, H.220, H.222 Ligands: FE.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.77, B:D.80, B:V.81, B:I.102, B:Y.106 Hydrogen bonds: B:Q.236 Salt bridges: B:R.217, B:H.220, B:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matera, I. et al., Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts. J.Struct.Biol. (2010)

Release Date

2010-01-12

Peptides

Catechol 1,2-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Catechol 1,2-dioxygenase

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