SMTL ID : 7wjr.1

Crystal structure of dihydroxybenzoate decarboxylase mutant A63S from Aspergillus oryzae in complex with catechol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.9, H.168, D.294 Ligands: CAQ.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.9, A:H.168, A:D.294, H2O.11 MG.3: 4 residues within 4Å: Chain B: E.9, H.168, D.294 Ligands: CAQ.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.9, B:H.168, B:D.294, H2O.27 MG.5: 4 residues within 4Å: Chain C: E.9, H.168, D.294 Ligands: CAQ.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.9, C:H.168, C:D.294, H2O.44 MG.7: 4 residues within 4Å: Chain D: E.9, H.168, D.294 Ligands: CAQ.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.9, D:H.168, D:D.294, H2O.59

4 x CAQ: CATECHOL(Non-covalent)

CAQ.2: 10 residues within 4Å: Chain A: W.24, F.28, S.64, H.168, P.190, F.194, D.294, F.297 Chain B: W.238 Ligands: MG.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.24, A:F.28, A:F.28, A:P.190, A:F.297, B:W.238 Hydrogen bonds: A:W.24 Water bridges: A:E.9, A:S.64, A:H.168, A:D.294 pi-Stacking: A:F.194, A:F.297 CAQ.4: 10 residues within 4Å: Chain A: W.238 Chain B: W.24, F.28, S.64, H.168, P.190, F.194, D.294, F.297 Ligands: MG.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.24, B:F.28, B:P.190, B:F.297, A:W.238 Water bridges: B:E.9, B:S.64, B:H.168 pi-Stacking: B:F.28, B:F.194, B:F.297 CAQ.6: 10 residues within 4Å: Chain C: W.24, F.28, S.64, H.168, P.190, F.194, D.294, F.297 Chain D: W.238 Ligands: MG.5 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.24, C:F.28, C:P.190, C:F.297, D:W.238 Hydrogen bonds: C:D.294 Water bridges: C:S.64, C:H.168 pi-Stacking: C:F.28, C:F.194, C:F.297 CAQ.8: 10 residues within 4Å: Chain C: W.238 Chain D: W.24, F.28, S.64, H.168, P.190, F.194, D.294, F.297 Ligands: MG.7 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.24, D:F.28, D:F.28, D:P.190, D:F.297, C:W.238 Hydrogen bonds: D:W.24 Water bridges: D:S.64, D:H.168, D:D.294, D:D.294 pi-Stacking: D:F.194, D:F.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, F. et al., Molecular mechanism of reversible decarboxylase with efficient CO2 fixation. To Be Published

Release Date

2023-01-18

Peptides

2,3-dihydroxybenzoate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2,3-dihydroxybenzoate decarboxylase