4IZJ

Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.

Structural Biology Knowledgebase: 4IZJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IZJ

Classification: HYDROLASE

Total Structure Weight: 112259.98

Macromolecule Entities
Molecule Chains Length Organism Details
Yellowtail Ascites Virus (YAV) VP4 protease A, E 210 Yellowtail ascites virus EC#: 3.4.21.115 IUBMB
Mutation: N616D
Gene Name(s):
Yellowtail Ascites Virus (YAV) VP4 protease B, C 210 Yellowtail ascites virus EC#: 3.4.21.115 IUBMB
Mutation: N616D
Gene Name(s):
Yellowtail Ascites Virus (YAV) VP4 protease D 210 Yellowtail ascites virus EC#: 3.4.21.115 IUBMB
Mutation: N616D
Gene Name(s):

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

D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

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

A 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, B, C, D, E L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.178
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.61 α = 90.00
b = 64.33 β = 95.80
c = 187.74 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: 3R0B

Revision History

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