SMTL ID : 5vgm.1

Crystal structure of dihydroorotase pyrC from Vibrio cholerae in complex with zinc at 1.95 A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: K.101, H.138, H.176 Ligands: ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.138, A:H.176, H2O.2 ZN.2: 5 residues within 4Å: Chain A: H.16, H.18, K.101, D.249 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.16, A:H.18, A:D.249, H2O.2 ZN.6: 4 residues within 4Å: Chain B: K.101, H.138, H.176 Ligands: ZN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.138, B:H.176, H2O.6 ZN.7: 5 residues within 4Å: Chain B: H.16, H.18, K.101, D.249 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.16, B:H.18, B:D.249, H2O.6

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: R.20, D.21, T.45, V.46 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.21 Hydrogen bonds: A:V.46, A:V.46 ACT.4: 4 residues within 4Å: Chain A: R.206, R.226 Chain B: R.206, R.226 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.206, A:R.226, B:R.206, B:R.226 ACT.5: 2 residues within 4Å: Chain A: D.300, R.306 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.306 ACT.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.327

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain B: G.285, K.286, L.287 Ligand excluded by PLIP

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

2017-04-26

Peptides

Dihydroorotase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotase