SMTL ID : 5znh.1

Catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.150, H.220, E.271 Ligands: MCT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.150, A:H.220, A:E.271 FE.6: 4 residues within 4Å: Chain B: H.150, H.220, E.271 Ligands: MCT.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.150, B:H.220, B:E.271 FE.11: 4 residues within 4Å: Chain C: H.150, H.220, E.271 Ligands: MCT.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.150, C:H.220, C:E.271 FE.16: 4 residues within 4Å: Chain D: H.150, H.220, E.271 Ligands: MCT.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.150, D:H.220, D:E.271

4 x MCT: 4-METHYLCATECHOL(Non-covalent)

MCT.2: 13 residues within 4Å: Chain A: H.150, F.198, H.206, H.220, H.252, I.254, T.255, Y.261, E.271, F.273, A.297, I.298 Ligands: FE.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.198, A:F.198, A:H.252, A:T.255, A:F.273, A:I.298 Hydrogen bonds: A:Y.261 pi-Stacking: A:H.252 MCT.7: 13 residues within 4Å: Chain B: H.150, F.198, H.206, H.220, H.252, I.254, T.255, Y.261, E.271, F.273, A.297, I.298 Ligands: FE.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.198, B:F.198, B:H.252, B:T.255, B:F.273, B:I.298 Hydrogen bonds: B:Y.261 pi-Stacking: B:H.252 MCT.12: 13 residues within 4Å: Chain C: H.150, F.198, H.206, H.220, H.252, I.254, T.255, Y.261, E.271, F.273, A.297, I.298 Ligands: FE.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.198, C:F.198, C:H.252, C:T.255, C:F.273, C:I.298 pi-Stacking: C:H.252 MCT.17: 13 residues within 4Å: Chain D: H.150, F.198, H.206, H.220, H.252, I.254, T.255, Y.261, E.271, F.273, A.297, I.298 Ligands: FE.16 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.198, D:F.198, D:H.252, D:T.255, D:F.273, D:I.298 pi-Stacking: D:H.252

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: G.162, N.164, D.168, I.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.164 PEG.8: 4 residues within 4Å: Chain B: G.162, N.164, D.168, I.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.164 PEG.13: 4 residues within 4Å: Chain C: G.162, N.164, D.168, I.193 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.164 PEG.18: 4 residues within 4Å: Chain D: G.162, N.164, D.168, I.193 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.164

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: H.65, T.97, L.98, R.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.116, A:R.116 EDO.9: 4 residues within 4Å: Chain B: H.65, T.97, L.98, R.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.116, B:R.116 EDO.14: 4 residues within 4Å: Chain C: H.65, T.97, L.98, R.116 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.116, C:R.116 EDO.19: 4 residues within 4Å: Chain D: H.65, T.97, L.98, R.116 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.116, D:R.116

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.149, T.204, H.206, D.207 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.204, A:H.206, A:D.207, H2O.1 CA.10: 4 residues within 4Å: Chain B: D.149, T.204, H.206, D.207 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.204, B:H.206, B:D.207, H2O.2 CA.15: 4 residues within 4Å: Chain C: D.149, T.204, H.206, D.207 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.204, C:H.206, C:D.207, H2O.3 CA.20: 4 residues within 4Å: Chain D: D.149, T.204, H.206, D.207 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.204, D:H.206, D:D.207, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, K. et al., catechol 2,3-dioxygenase with 4-methyl catechol from Diaphorobacter sp DS2. To Be Published

Release Date

2019-04-17

Peptides

Catechol 2,3-dioxygenase, extradiol protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Catechol 2,3-dioxygenase, extradiol protein

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