SMTL ID : 6cty.3 (2 other biounits)

Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.127, H.164, H.202 Ligands: ZN.2, MLT.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.164, A:H.202 ZN.2: 6 residues within 4Å: Chain A: H.41, H.43, K.127, D.275 Ligands: ZN.1, MLT.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.41, A:H.43, A:D.275 ZN.4: 6 residues within 4Å: Chain B: H.41, H.43, K.127, D.275 Ligands: ZN.5, MLT.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.41, B:H.43, B:D.275 ZN.5: 5 residues within 4Å: Chain B: K.127, H.164, H.202 Ligands: ZN.4, MLT.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.164, B:H.202

2 x MLT: D-MALATE(Non-covalent)

MLT.3: 17 residues within 4Å: Chain A: H.41, H.43, R.45, N.69, K.127, T.134, T.135, H.164, H.202, L.247, D.275, A.277, H.279, A.291, G.292 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.69, A:T.135, A:T.135, A:A.291 Water bridges: A:L.247, A:L.247 Salt bridges: A:H.43, A:H.43, A:R.45, A:H.164, A:H.202, A:H.279 MLT.6: 16 residues within 4Å: Chain B: H.41, H.43, R.45, N.69, K.127, T.134, T.135, H.164, H.202, L.247, D.275, A.277, H.279, A.291 Ligands: ZN.4, ZN.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.69, B:T.134, B:T.134, B:T.135, B:A.291 Water bridges: B:L.247, B:L.247 Salt bridges: B:H.43, B:H.43, B:R.45, B:H.164, B:H.202, B:H.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lipowska, J. et al., Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. Int.J.Biol.Macromol. (2019)

Release Date

2018-04-04

Peptides

Dihydroorotase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dihydroorotase

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