4DOQ | pdb_00004doq

Crystal structure of the complex of Porcine Pancreatic Trypsin with 1/2SLPI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure basis 1/2SLPI and porcine pancreas trypsin interaction

Fukushima, K.Kamimura, T.Takimoto-Kamimura, M.

(2013) J Synchrotron Radiat 20: 943-947

  • DOI: https://doi.org/10.1107/S090904951302133X
  • Primary Citation Related Structures: 
    4DOQ

  • PubMed Abstract: 

    SLPI (secretory leukocyte protease inhibitor) is a 107-residue protease inhibitor which inhibits various serine proteases, including elastase, cathepsin G, chymotrypsin and trypsin. SLPI is obtained as a multiple inhibitor in lung defense and in chronic airway infection. X-ray crystal structures have so far reported that they are full-length SLPIs with bovine α-chymotrypsin and 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58-Ala107) with HNE (human neutrophil elastase). To understand the role of this multiple inhibitory mechanism, the crystal structure of 1/2SLPI with porcine pancreas trypsin was solved and the binding modes of two other complexes compared. The Leu residue surprisingly interacts with the S1 site of trypsin, as with chymotrypsin and elastase. The inhibitory mechanism of 1/2SLPI using the wide primary binding site contacts (from P2' to P5) with various serine proteases is discussed. These inhibitory mechanisms have been acquired in the evolution of the protection system for acute inflammatory diseases.


  • Organizational Affiliation
    • Medicinal Chemistry Technology Department, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan.

Macromolecule Content 

  • Total Structure Weight: 82.29 kDa 
  • Atom Count: 6,178 
  • Modeled Residue Count: 754 
  • Deposited Residue Count: 763 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trypsin
A, C, E
223Sus scrofaMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa)
Explore P00761 
Go to UniProtKB:  P00761
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00761
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antileukoproteinase
B, D
47Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P03973 (Homo sapiens)
Explore P03973 
Go to UniProtKB:  P03973
PHAROS:  P03973
GTEx:  ENSG00000124107 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03973
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XPE

Query on XPE



Download:Ideal Coordinates CCD File
F [auth A]3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
K [auth C]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
J [auth B]
L [auth C]
N [auth D]
G [auth A],
H [auth A],
J [auth B],
L [auth C],
N [auth D],
O [auth D],
P [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A],
M [auth C],
Q [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.535α = 90
b = 118.61β = 90.74
c = 93.393γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
d*TREKdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary