1JRR

HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUTANT] COMPLEXED WITH PEPTIDE MIMIckING THE REACTIVE CENTER LOOP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

CRYSTAL STRUCTURE OF THE COMPLEX OF PLASMINOGEN ACTIVATOR INHIBITOR 2 WITH A PEPTIDE MIMICKING THE REACTIVE CENTER LOOP

JANKOVA, L.HARROP, S.J.SAUNDERS, D.N.ANDREWS, J.L.BERTRAM, K.C.GOULD, A.R.BAKER, M.S.CURMI, P.M.G.

(2001) J.Biol.Chem. 276: 43374-43382

  • DOI: 10.1074/jbc.M103021200

  • PubMed Abstract: 
  • The structure of the serpin, plasminogen activator inhibitor type-2 (PAI-2), in a complex with a peptide mimicking its reactive center loop (RCL) has been determined at 1.6-A resolution. The structure shows the relaxed state serpin structure with a p ...

    The structure of the serpin, plasminogen activator inhibitor type-2 (PAI-2), in a complex with a peptide mimicking its reactive center loop (RCL) has been determined at 1.6-A resolution. The structure shows the relaxed state serpin structure with a prominent six-stranded beta-sheet. Clear electron density is seen for all residues in the peptide. The P1 residue of the peptide binds to a well defined pocket at the base of PAI-2 that may be important in determining the specificity of protease inhibition. The stressed-to-relaxed state (S --> R) transition in PAI-2 can be modeled as the relative motion between a quasirigid core domain and a smaller segment comprising helix hF and beta-strands s1A, s2A, and s3A. A comparison of the Ramachandran plots of the stressed and relaxed state PAI-2 structures reveals the location of several hinge regions connecting these two domains. The hinge regions cluster in three locations on the structure, ensuring a cooperative S --> R transition. We hypothesize that the hinge formed by the conserved Gly(206) on beta-strand s3A in the breach region of PAI-2 effects the S --> R transition by altering its backbone torsion angles. This torsional change is due to the binding of the P14 threonine of the RCL to the open breach region of PAI-2.


    Related Citations: 
    • INTERACTION BETWEEN THE P14 RESIDUE AND STRAND 2 OF BETA-SHEET B IS CRITICAL FOR REACTIVE CENTER LOOP INSERTION IN PAI-2
      SAUNDERS, D.N.,GOULD, A.R.,RANSON, M.,JANKOVA, L.,HARROP, S.J.,G CURMI, P.M.,BAKER, M.S.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Initiative in Biomolecular Structure, School of Physics, University of New South Wales, Sydney New South Wales 2052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN ACTIVATOR INHIBITOR-2
A
382Homo sapiensGene Names: SERPINB2 (PAI2, PLANH2)
Find proteins for P05120 (Homo sapiens)
Go to Gene View: SERPINB2
Go to UniProtKB:  P05120
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN ACTIVATOR INHIBITOR-2
P
15Homo sapiensGene Names: SERPINB2 (PAI2, PLANH2)
Find proteins for P05120 (Homo sapiens)
Go to Gene View: SERPINB2
Go to UniProtKB:  P05120
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.139α = 90.00
b = 104.160β = 90.00
c = 41.395γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance