1N51

Aminopeptidase P in complex with the inhibitor apstatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Escherichia coli aminopeptidase P in complex with the inhibitor apstatin.

Graham, S.C.Maher, M.J.Simmons, W.H.Freeman, H.C.Guss, J.M.

(2004) Acta Crystallogr.,Sect.D 60: 1770-1779

  • DOI: 10.1107/S0907444904018724

  • PubMed Abstract: 
  • Aminopeptidase P (APPro) is a metalloprotease whose active site includes a dinuclear manganese(II) cluster. The enzyme cleaves the N-terminal residue from a polypeptide when the second residue is proline. A complex of Escherichia coli APPro (EcAPPro) ...

    Aminopeptidase P (APPro) is a metalloprotease whose active site includes a dinuclear manganese(II) cluster. The enzyme cleaves the N-terminal residue from a polypeptide when the second residue is proline. A complex of Escherichia coli APPro (EcAPPro) with an inhibitor, apstatin [N-(2S,3R)-3-amino-2-hydroxy-4-phenyl-butanoyl-L-prolyl-L-prolyl-L-alaninamide], has been crystallized. Apstatin binds to the active site of EcAPPro with its N-terminal amino group coordinated to one of the two Mn(II) atoms at the metal centre. The apstatin hydroxyl group replaces a hydroxide ion which bridges the two metal atoms in the native enzyme. The first proline residue of apstatin lies in a small hydrophobic cleft. The structure of the apstatin-EcAPPro complex has been refined at 2.3 A resolution with residuals R = 0.179 and R(free) = 0.204. The structure of the complex illustrates how apstatin inhibits APPro and suggests how substrates may bind to the enzyme, but the basis of the proline-specificity remains elusive.


    Related Citations: 
    • Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
      Brunger, A.T.,Adams, P.D.,Clore, G.M.,Delano, W.L.,Gros, P.,Grosse-Kunstleve, R.,Jiang, J.-S.,Kuszewski, J.,Nilges, M.,Pannu, N.S.,Read, R.J.,Rice, L.M.,Simonson, T.,Warren, G.
      (1998) Acta Crystallogr.,Sect.D 54: 905


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xaa-Pro aminopeptidase
A
440Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pepP
EC: 3.4.11.9
Find proteins for P15034 (Escherichia coli (strain K12))
Go to UniProtKB:  P15034
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
apstatin
B
5N/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
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000553
Query on PRD_000553
BAPSTATINPeptide-like / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATNKi: 14000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.319α = 90.00
b = 139.319β = 90.00
c = 231.005γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    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: 2012-12-12
    Type: Other