2YOL

West Nile Virus NS2B-NS3 protease in complex with 3,4- dichlorophenylacetyl-Lys-Lys-GCMA

Structural Biology Knowledgebase: 2YOL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YOL

Classification: HYDROLASE

Total Structure Weight: 25310.31

Macromolecule Entities
Molecule Chains Length Organism Details
SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3 A 230 West nile virus EC#: 3.4.21.91 IUBMB 3.6.1.15 IUBMB 3.6.4.13 IUBMB
Fragment: NS2B, RESIDUES 1420-1466,AND NS3,1502-1671
Details: RESIDUES SER47 TO PRO91 BELONG TO NS2B, WHICH WE DESIGNATED AS MOLECULE A IN THE ASSOCIATED PUBLICATION. RESIDUES GLY1002 TO GLU1169 (RESIDUE NUMBERS WERE INCREMENTED BY 1000) BELONG TO NS3, WHICH WE DESIGNATED AS MOLECULE B IN THE ASSOCIATED PUBLICATION.
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A (S)-6-amino-N-((S)-6-amino-1-(((1r,4S)-4- guanidinocyclohexyl)methylamino)-1-oxohexan- 2-yl)-2-(2-(3,4-dichlorophenyl)acetamido)hexanamide
3,4-dichlorophenylacetyl-Lys-Lys-GCMA (Synonym)
C28 H46 Cl2 N8 O3
OWKCLMWSCHVRNJ-BTDFZRAWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EBN Ki: 130 nM (86) BindingDB

N/A in BindingMoad
Ki: 130 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.188
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 118.70 α = 90.00
b = 118.70 β = 90.00
c = 66.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-25
  • Released Date: 2013-03-27
  • Deposition author(s): Hammamy, M.Z., Haase, C., Hammami, M., Hilgenfeld, R., Steinmetzer, T.

Revision History

No revisions since initial release