SMTL ID : 2fvk.1

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.61, H.63, K.166, H.254, D.357 Ligands: ZN.2, DUC.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.61, A:H.63, A:D.357 ZN.2: 7 residues within 4Å: Chain A: K.166, F.168, H.198, H.254, S.330 Ligands: ZN.1, DUC.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.198, A:H.254 ZN.4: 5 residues within 4Å: Chain B: H.61, H.63, D.357 Ligands: ZN.5, DUC.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.61, B:H.63, B:D.357 ZN.5: 6 residues within 4Å: Chain B: K.166, F.168, H.198, H.254 Ligands: ZN.4, DUC.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.198, B:H.254 ZN.7: 7 residues within 4Å: Chain C: H.61, H.63, K.166, H.254, D.357 Ligands: ZN.8, DUC.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.61, C:H.63, C:D.357 ZN.8: 6 residues within 4Å: Chain C: K.166, F.168, H.198, H.254 Ligands: ZN.7, DUC.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.198, C:H.254 ZN.10: 7 residues within 4Å: Chain D: H.61, H.63, K.166, H.254, D.357 Ligands: ZN.11, DUC.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.61, D:H.63, D:D.357 ZN.11: 8 residues within 4Å: Chain D: K.166, F.168, Y.171, H.198, H.254, S.330 Ligands: ZN.10, DUC.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.198, D:H.254

4 x DUC: DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE(Non-covalent)

DUC.3: 15 residues within 4Å: Chain A: H.61, H.63, L.71, K.166, Y.171, H.198, H.254, C.329, S.330, D.357, C.359, N.391, G.392 Ligands: ZN.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.330, A:S.330, A:N.391 DUC.6: 10 residues within 4Å: Chain B: H.198, H.254, C.329, S.330, D.357, C.359, N.391, G.392 Ligands: ZN.4, ZN.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.330, B:S.330 DUC.9: 12 residues within 4Å: Chain C: H.63, Y.171, H.198, H.254, C.329, S.330, D.357, C.359, N.391, G.392 Ligands: ZN.7, ZN.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.330, C:S.330, C:N.391 DUC.12: 14 residues within 4Å: Chain D: H.61, H.63, L.71, K.166, Y.171, H.254, C.329, S.330, D.357, C.359, N.391, G.392 Ligands: ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.171, D:S.330, D:S.330, D:N.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lohkamp, B. et al., The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity. J.Biol.Chem. (2006)

Release Date

2006-03-14

Peptides

dihydropyrimidinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

dihydropyrimidinase

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