1OT5

The 2.4 Angstrom Crystal Sructure of Kex2 in complex with a peptidyl-boronic acid inhibitor

Structural Biology Knowledgebase: 1OT5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1OT5

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 106700.43

Macromolecule Entities
Molecule Chains Length Organism Details
Kexin A, B 477 Saccharomyces cerevisiae EC#: 3.4.21.61 IUBMB
Fragment: residue 123-599
Gene Name(s): KEX2 QDS1 YNL238W N1122
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ac-Ala-Lys-boroArg N-acetylated boronic acid peptide inhibitor C, D 4 synthetic

Small Molecules
Ligands 2 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)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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_000411
Query on PRD_000411
C, D N-acetyl-L-alanyl-6-ammonio-N-[(1R)-4-carbamimidamido-1-(dihydroxyboranyl)butyl]-L-norleucinamide Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.209
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 113.84 α = 90.00
b = 113.84 β = 90.00
c = 370.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-21
  • Released Date: 2003-06-17
  • Deposition author(s): Holyoak, T., Wilson, M.A., Fenn, T.D., Kettner, C.A., Petsko, G.A., Fuller, R.S., Ringe, D.

Revision History

  • 2013-02-20
    Type: Other | Details: update cell parameters
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description