1POP

X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A PAPAIN-LEUPEPTIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

X-ray crystallographic structure of a papain-leupeptin complex.

Schroder, E.Phillips, C.Garman, E.Harlos, K.Crawford, C.

(1993) FEBS Lett. 315: 38-42


  • PubMed Abstract: 
  • The three-dimensional structure of the papain-leupeptin complex has been determined by X-ray crystallography to a resolution of 2.1 A (overall R-factor = 19.8%). The structure indicates that: (i) leupeptin contacts the S subsites of the papain active ...

    The three-dimensional structure of the papain-leupeptin complex has been determined by X-ray crystallography to a resolution of 2.1 A (overall R-factor = 19.8%). The structure indicates that: (i) leupeptin contacts the S subsites of the papain active site and not the S' subsites; (ii) the 'carbonyl' carbon atom of the inhibitor is covalently bound by the Cys-25 sulphur atom of papain and is tetrahedrally coordinated; (iii) the 'carbonyl' oxygen atom of the inhibitor faces the oxyanion hole and makes hydrogen bond contacts with Gln-19 and Cys-25.


    Related Citations: 
    • The Structure of Papain Refined at 1.65 Angstroms
      Kamphuis, I.G.,Kalk, K.H.,Swarte, M.B.A.,Drenth, J.
      (1984) J.Mol.Biol. 179: 233


    Organizational Affiliation

    University of Oxford, Laboratory of Molecular Biophysics, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PAPAIN
A
212Carica papayaMutation(s): 0 
EC: 3.4.22.2
Find proteins for P00784 (Carica papaya)
Go to UniProtKB:  P00784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEUPEPTIN
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOH
Query on MOH

Download SDF File 
Download CCD File 
A, B
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000216 (SVC)
Query on PRD_000216
BLEUPEPTINOligopeptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.920α = 90.00
b = 104.960β = 90.00
c = 50.970γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Type: Other
  • Version 1.4: 2014-04-02
    Type: Source and taxonomy
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other