4IZK

Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an acyl-enzyme complex and an empty active site

Structural Biology Knowledgebase: 4IZK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IZK

Classification: HYDROLASE

Total Structure Weight: 44649.74

Macromolecule Entities
Molecule Chains Length Organism Details
Yellowtail Ascites Virus (YAV) VP4 protease A 210 Yellowtail ascites virus EC#: 3.4.21.115 IUBMB
Mutation: K674A
Gene Name(s):
Yellowtail Ascites Virus (YAV) VP4 protease B 210 Yellowtail ascites virus EC#: 3.4.21.115 IUBMB
Mutation: K674A
Gene Name(s):

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

B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.173
  • Space Group: F 41 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 273.52 α = 90.00
b = 273.52 β = 90.00
c = 273.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-30
  • Released Date: 2013-02-27
  • Deposition author(s): Paetzel, M., Chung, I.Y.W.
  • Previous versions: 3RBP 4HHC

Revision History

  • 2013-05-22
    Type: Citation | Details: Citation update
  • 2013-04-03
    Type: Citation | Details: Citation update