SMTL ID : 8wq9.1

Crystal structure of dihydropyrimidinase complexed with gamma-aminobutyric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

4 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.1: 7 residues within 4Å: Chain A: F.66, S.333, K.334, I.335, P.336, N.337 Ligands: ABU.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.66, A:N.337 Hydrogen bonds: A:S.333, A:N.337, A:N.337 ABU.2: 12 residues within 4Å: Chain A: H.61, L.64, I.95, K.150, F.152, Y.155, I.159, D.316, C.318 Ligands: ABU.1, ZN.3, ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.152 Salt bridges: A:H.61 ABU.5: 8 residues within 4Å: Chain B: F.66, F.320, S.333, K.334, I.335, P.336, N.337 Ligands: ABU.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:N.337 Hydrogen bonds: B:S.333, B:N.337 ABU.6: 12 residues within 4Å: Chain B: H.61, L.64, I.95, K.150, F.152, Y.155, I.159, D.316, C.318 Ligands: ABU.5, ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.64, B:F.152, B:Y.155 Salt bridges: B:H.61

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.59, K.150, H.183, H.239 Ligands: ABU.2, ZN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.183 ZN.4: 6 residues within 4Å: Chain A: H.59, H.61, K.150, D.316 Ligands: ABU.2, ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.59, A:H.61, A:D.316, ABU.2 ZN.7: 5 residues within 4Å: Chain B: K.150, H.183, H.239 Ligands: ABU.6, ZN.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.183 ZN.8: 6 residues within 4Å: Chain B: H.59, H.61, K.150, D.316 Ligands: ABU.6, ZN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.59, B:H.61, B:D.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y.H. et al., The complexed crystal structure of dihydropyrimidinase reveals a potential interactive link with the neurotransmitter gamma-aminobutyric acid (GABA). Biochem.Biophys.Res.Commun. (2024)

Release Date

2024-04-03

Peptides

D-hydantoinase/dihydropyrimidinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-hydantoinase/dihydropyrimidinase

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