6BJD

Crystal Structure of Human Calpain-3 Protease Core in Complex with E-64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of human calpain-3 protease core with and without bound inhibitor reveal mechanisms of calpain activation.

Ye, Q.Campbell, R.L.Davies, P.L.

(2018) J. Biol. Chem. 293: 4056-4070


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calpain-3
A, B, C, D
382Homo sapiensMutation(s): 0 
Gene Names: CAPN3 (CANP3, CANPL3, NCL1)
EC: 3.4.22.54
Find proteins for P20807 (Homo sapiens)
Go to Gene View: CAPN3
Go to UniProtKB:  P20807
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
E64
Query on E64

Download SDF File 
Download CCD File 
A, B, C, D
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
C15 H30 N5 O5
QPQNJAXBPHVASB-QWRGUYRKSA-O
 Ligand Interaction
SOR
Query on SOR

Download SDF File 
Download CCD File 
B
D-SORBITOL
C6 H14 O6
FBPFZTCFMRRESA-JGWLITMVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.280α = 90.00
b = 105.360β = 90.00
c = 225.360γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP 74681

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references