1R64

The 2.2 A crystal structure of Kex2 protease in complex with Ac-Arg-Glu-Lys-boroArg peptidyl boronic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1R64

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 108743.85

Macromolecule Entities
Molecule Chains Length Organism Details
Kexin A, B 481 Saccharomyces cerevisiae EC#: 3.4.21.61 IUBMB
Fragment: Residues 121-601
Gene Name(s): KEX2 QDS1 YNL238W N1122
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ac-Arg-Glu-Lys-boroArg peptide inhibitor C, D 5 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BTB
Query on BTB

B 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- PROPANE-1,3-DIOL
BIS-TRIS BUFFER (Synonym)
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000420
Query on PRD_000420
C, D AC-ARG-GLU-LYS-BOROARG PEPTIDYL BORONIC ACID Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.197
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 113.54 α = 90.00
b = 113.54 β = 90.00
c = 364.97 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-10-14
  • Released Date: 2004-03-09
  • Deposition author(s): Holyoak, T., Kettner, C.A., Petsko, G.A., Fuller, R.S., Ringe, D.

Revision History

  • 2008-04-29
    Type: Version format compliance
  • 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • 2011-11-16
    Type: Atomic model
  • 2012-12-12
    Type: Other