1BP4

USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES.

Structural Biology Knowledgebase: 1BP4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1BP4

Classification: HYDROLASE

Total Structure Weight: 23927.16

Macromolecule Entities
Molecule Chains Length Organism Details
PAPAIN A 212 Carica papaya EC#: 3.4.22.2 IUBMB
Fragment: NON
Mutation: E47Q, E118Q, E135Q
Details: ALDEHYDE INHIBITOR COVALENTLY BOUND TO ACTIVE SITE CYS 25 AS A HEMIMERCAPTAL. BOND OCCURS BETWEEN CYS 25-SG AND ALD 213-C22
Gene Name(s):

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ALD
Query on ALD

A N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)- 1-hydroxy-4-methylpentan-2-yl]-L-leucinamide
C26 H43 N3 O5
WUJQMWDTZKIKQZ-VABKMULXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 100.54 α = 90.00
b = 50.74 β = 99.90
c = 62.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-08-12
  • Released Date: 1999-08-12
  • Deposition author(s): Lalonde, J.M., Zhao, B., Smith, W.W., Janson, C.A., Desjarlais, R.L., Tomaszek, T.A., Carr, T.J., Thompson, S.K., Yamashita, D.S., Veber, D.F., Abdel-Mequid, S.S.

Revision History

  • 2012-02-08
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4