6PAD

Binding of chloromethyl ketone substrate analogues to crystalline papain

Structural Biology Knowledgebase: 6PAD SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 6PAD

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 23852.39

Macromolecule Entities
Molecule Chains Length Organism Details
PAPAIN A 212 Carica papaya EC#: 3.4.22.2 IUBMB
Mutation: E47Q, E118Q, E135Q
Gene Name(s):

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0PC
Query on 0PC

A Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro- 1-methyl-2-oxopropyl]-L-phenylalaninamide
ZPACK (Synonym)
C21 H23 Cl N2 O4
YAWCSFNDFRSZKD-YJBOKZPZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000333 (PHE,PHQ,ALA,0QE) A BENZYLOXYCARBONYL-PHENYLALANYL-METHYLENYLALANYL Peptide-like /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Observed:
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 45.00 α = 90.00
b = 104.30 β = 90.00
c = 50.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1976-11-01
  • Released Date: 1977-04-12
  • Deposition author(s): Drenth, J., Kalk, K.H., Swen, H.M.
  • Previous versions: 7PAP

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Flag nonstandard coordinate frame | Details: Tagged nonstandard coordinate frame