SMTL ID : 7wkl.1

Crystal structure of dihydroxybenzoate decarboxylase mutant F296Y from Aspergillus oryzae in complex with catechol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.9, A:H.168, A:D.294, H2O.1, H2O.10 MG.4: 4 residues within 4Å: Chain B: E.9, H.168, D.294 Ligands: CAQ.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.9, B:H.168, B:D.294, H2O.20, H2O.21 MG.7: 4 residues within 4Å: Chain C: E.9, H.168, D.294 Ligands: CAQ.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.9, C:H.168, C:D.294, H2O.33, H2O.40 MG.10: 4 residues within 4Å: Chain D: E.9, H.168, D.294 Ligands: CAQ.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.9, D:H.168, D:D.294, H2O.50, H2O.55

4 x CAQ: CATECHOL(Non-covalent)

CAQ.2: 10 residues within 4Å: Chain A: W.24, F.28, A.64, H.168, P.190, F.194, D.294, Y.297 Chain B: W.238 Ligands: MG.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.24, A:F.28, A:P.190, A:Y.297, B:W.238 Hydrogen bonds: A:D.294 Water bridges: A:T.63, A:A.64 pi-Stacking: A:F.28, A:F.194, A:Y.297 CAQ.5: 10 residues within 4Å: Chain A: W.238 Chain B: W.24, F.28, A.64, H.168, P.190, F.194, D.294, Y.297 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.24, B:F.28, B:F.28, B:P.190, B:Y.297, A:W.238 Hydrogen bonds: B:W.24, B:H.168 Water bridges: B:T.63 pi-Stacking: B:F.194, B:Y.297 CAQ.8: 10 residues within 4Å: Chain C: W.24, F.28, A.64, H.168, P.190, F.194, D.294, Y.297 Chain D: W.238 Ligands: MG.7 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.24, C:F.28, C:F.28, C:P.190, C:Y.297, D:W.238 Hydrogen bonds: C:D.294 Water bridges: C:T.63, C:A.64 pi-Stacking: C:F.194, C:Y.297 CAQ.11: 10 residues within 4Å: Chain C: W.238 Chain D: W.24, F.28, A.64, H.168, P.190, F.194, D.294, Y.297 Ligands: MG.10 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.24, D:F.28, D:F.28, D:P.190, D:Y.297, C:W.238 Hydrogen bonds: D:D.294 Water bridges: D:E.9, D:T.63, D:T.63 pi-Stacking: D:F.194, D:Y.297

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: H.49, K.52, H.53, S.301 9 PLIP interactions: 9 interactions with chain A Water bridges: A:E.48, A:H.49, A:F.300, A:S.301, A:S.301, A:S.301 Salt bridges: A:H.49, A:K.52, A:H.53 SO4.6: 4 residues within 4Å: Chain B: H.49, K.52, H.53, S.301 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.301 Salt bridges: B:H.49, B:K.52, B:H.53 SO4.9: 3 residues within 4Å: Chain C: H.49, K.52, H.53 5 PLIP interactions: 5 interactions with chain C Water bridges: C:F.300, C:S.301 Salt bridges: C:H.49, C:K.52, C:H.53 SO4.12: 4 residues within 4Å: Chain D: H.49, K.52, H.53, S.301 7 PLIP interactions: 7 interactions with chain D Water bridges: D:H.49, D:T.299, D:S.301, D:S.301 Salt bridges: D:H.49, D:K.52, D:H.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, Y. et al., The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase. Appl.Microbiol.Biotechnol. (2023)

Release Date

2023-01-25

Peptides

Amidohydrolase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Amidohydrolase 2