8ZCR

Structure of PI9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: in silico
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Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8H4X


Literature

Crystallization and crystallographic studies of human serine protease inhibitor (serpin) B9.

Yan, T.Zhou, A.

(2024) Acta Crystallogr F Struct Biol Commun 80: 286-293

  • DOI: https://doi.org/10.1107/S2053230X24009439
  • Primary Citation of Related Structures:  
    8ZCR

  • PubMed Abstract: 

    Serine protease inhibitor B9 (serpin B9, also known as protease inhibitor 9 or PI9) plays a critical role in regulating the immune response by specifically inhibiting granzyme B, a serine protease found in cytotoxic T lymphocytes and natural killer cells. Despite its potential as an anticancer drug target, the structural details of serpin B9 have remained elusive until now. In this study, a cleaved form of recombinant human serpin B9 was successfully prepared and crystallized. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 68.51, b = 82.32, c = 101.17 Å, and an X-ray diffraction data set was collected at 1.9 Å resolution. The structure shows that serpin B9 adopts a relaxed conformation, with its cleaved reactive-centre loop inserted into the central β-sheet. Unlike other serpins, serpin B9 shows significant structural deviations around helix D, with a larger surface cavity, which could serve as a promising target for small-molecule inhibitors.


  • Organizational Affiliation

    Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serpin B9341Homo sapiensMutation(s): 0 
Gene Names: SERPINB9PI9
UniProt & NIH Common Fund Data Resources
Find proteins for P50453 (Homo sapiens)
Explore P50453 
Go to UniProtKB:  P50453
PHAROS:  P50453
GTEx:  ENSG00000170542 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50453
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serpin B937Homo sapiensMutation(s): 0 
Gene Names: SERPINB9PI9
UniProt & NIH Common Fund Data Resources
Find proteins for P50453 (Homo sapiens)
Explore P50453 
Go to UniProtKB:  P50453
PHAROS:  P50453
GTEx:  ENSG00000170542 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50453
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
U [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.512α = 90
b = 82.323β = 90
c = 101.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81870309
National Natural Science Foundation of China (NSFC)China32070934

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release