1BY7 | pdb_00001by7

HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.268 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: implications for serpin function.

Harrop, S.J.Jankova, L.Coles, M.Jardine, D.Whittaker, J.S.Gould, A.R.Meister, A.King, G.C.Mabbutt, B.C.Curmi, P.M.

(1999) Structure 7: 43-54

  • DOI: https://doi.org/10.1016/s0969-2126(99)80008-2
  • Primary Citation Related Structures: 
    1BY7

  • PubMed Abstract: 

    Plasminogen activator inhibitor 2 (PAI-2) is a member of the serpin family of protease inhibitors that function via a dramatic structural change from a native, stressed state to a relaxed form. This transition is mediated by a segment of the serpin termed the reactive centre loop (RCL); the RCL is cleaved on interaction with the protease and becomes inserted into betasheet A of the serpin. Major questions remain as to what factors facilitate this transition and how they relate to protease inhibition. The crystal structure of a mutant form of human PAI-2 in the stressed state has been determined at 2.0 A resolution. The RCL is completely disordered in the structure. An examination of polar residues that are highly conserved across all serpins identifies functionally important regions. A buried polar cluster beneath betasheet A (the so-called 'shutter' region) is found to stabilise both the stressed and relaxed forms via a rearrangement of hydrogen bonds. A statistical analysis of interstrand interactions indicated that the shutter region can be used to discriminate between inhibitory and non-inhibitory serpins. This analysis implied that insertion of the RCL into betasheet A up to residue P8 is important for protease inhibition and hence the structure of the complex formed between the serpin and the target protease.


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

Macromolecule Content 

  • Total Structure Weight: 43.05 kDa 
  • Atom Count: 3,045 
  • Modeled Residue Count: 354 
  • Deposited Residue Count: 382 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)382Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05120 (Homo sapiens)
Explore P05120 
Go to UniProtKB:  P05120
PHAROS:  P05120
GTEx:  ENSG00000197632 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05120
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.268 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.82α = 90
b = 41.73β = 114.88
c = 77.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-11-13
    Changes: Structure summary