5VGM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 5VGM

Classification: HYDROLASE

Total Structure Weight: 76241.16

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydroorotase A, B 345 Vibrio cholerae EC#: 3.5.2.3 IUBMB
Gene Name(s): pyrC VC_A0925
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B L-PEPTIDE LINKING C7 H14 N2 O4 LYS
CSX
Query on CSX
A, B L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 62.51 α = 90.00
b = 57.26 β = 105.09
c = 87.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-11
  • Released Date: 2017-04-26
  • Deposition author(s): Lipowska, J., Shabalin, I.G., Miks, C.D., Winsor, J., Cooper, D.R., Shuvalova, L., Kwon, K., Lewinski, K., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2017-04-26

    Type: Initial release

  • Version 1_1: 2017-09-13

    Type: Author supporting evidence