1PE6

REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION

Structural Biology Knowledgebase: 1PE6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.159

Literature

Macromolecules
Sequence Display for 1PE6

Classification: HYDROLASE (SULFHYDRYL PROTEINASE)

Total Structure Weight: 24214.50

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):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
E6C
Query on E6C

A N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO- 2-METHYL-BUTANE
C15 H28 N2 O5
KBIWEWPGBHKYML-RYUDHWBXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MOH
Query on MOH

A METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
E6C Ki: 2400 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.159
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.90 α = 90.00
b = 95.51 β = 90.00
c = 49.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1991-05-14
  • Released Date: 1993-04-15
  • Deposition author(s): Yamamoto, D., Matsumoto, K., Ohishi, H., Ishida, T., Inoue, M., Kitamura, K., Mizuno, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4