1LQ8

Crystal structure of cleaved protein C inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of Protein C Inhibitor Provides Insights into Hormone Binding and Heparin Activation

Huntington, J.A.Kjellberg, M.Stenflo, J.

(2003) Structure 11: 205-211

  • DOI: 10.1016/s0969-2126(02)00944-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein C inhibitor (PCI) is a member of the serpin family that has many biological functions. In blood it acts as a procoagulant, and, in the seminal vesicles, it is required for spermatogenesis. The activity of PCI is affected by heparin binding in ...

    Protein C inhibitor (PCI) is a member of the serpin family that has many biological functions. In blood it acts as a procoagulant, and, in the seminal vesicles, it is required for spermatogenesis. The activity of PCI is affected by heparin binding in a manner unique among the heparin binding serpins, and, in addition, PCI binds hydrophobic hormones with apparent specificity for retinoids. Here we present the 2.4 A crystallographic structure of reactive center loop (RCL) cleaved PCI. A striking feature of the structure is a two-turn N-terminal shortening of helix A, which creates a large hydrophobic pocket that docking studies indicate to be the retinoid binding site. On the basis of surface electrostatic properties, a novel mechanism for heparin activation is proposed.


    Organizational Affiliation

    Department of Haematology, Division of Structural Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, CB2 2XY, Cambridge, United Kingdom. jah52@cam.ac.uk



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
plasma serine protease inhibitorA, C, E, G346Homo sapiensMutation(s): 0 
Gene Names: SERPINA5PCIPLANH3PROCI
Find proteins for P05154 (Homo sapiens)
Explore P05154 
Go to UniProtKB:  P05154
NIH Common Fund Data Resources
PHAROS  P05154
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
plasma serine protease inhibitorB, D, F, H31Homo sapiensMutation(s): 0 
Gene Names: SERPINA5PCIPLANH3PROCI
Find proteins for P05154 (Homo sapiens)
Explore P05154 
Go to UniProtKB:  P05154
NIH Common Fund Data Resources
PHAROS  P05154
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, M
2 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K
2 N-Glycosylation
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
L
3 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
C, G
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A, C, G
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.2α = 90
b = 244.03β = 91.98
c = 66.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary