SMTL ID : 7ca1.2 (1 other biounit)

Crystal structure of dihydroorotase in complex with plumbagin from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-dimer

Ligands

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.1: 15 residues within 4Å: Chain A: H.16, R.18, N.43, K.98, T.105, T.106, H.137, K.230, D.258, A.260, H.262, A.275, G.276 Ligands: ZN.2, ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.260 Hydrogen bonds: A:N.43, A:T.105, A:T.106 Salt bridges: A:H.16, A:R.18, A:H.137, A:H.180, A:H.262

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.14, H.16, K.98, D.258 Ligands: LMR.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.14, A:H.16, A:D.258 ZN.3: 5 residues within 4Å: Chain A: K.98, H.137, H.180 Ligands: LMR.1, ZN.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.137, A:H.180 ZN.5: 5 residues within 4Å: Chain B: K.98, H.137, H.180 Ligands: 90R.4, ZN.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.137, B:H.180 ZN.6: 6 residues within 4Å: Chain B: H.14, H.16, K.98, D.258 Ligands: 90R.4, ZN.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.14, B:H.16, B:D.258

1 x 90R: 5-hydroxy-2-methylnaphthalene-1,4-dione(Non-covalent)

90R.4: 14 residues within 4Å: Chain B: H.16, R.18, N.43, K.98, Y.100, T.105, T.106, N.107, H.137, K.230, D.258, A.260 Ligands: ZN.5, ZN.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.43, B:T.105, B:T.106, B:N.107, B:K.230 Hydrogen bonds: B:R.18, B:D.258 pi-Stacking: B:H.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, H.H. et al., Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis. Int J Mol Sci (2021)

Release Date

2021-06-09

Peptides

Dihydroorotase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Dihydroorotase

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