1OKX | pdb_00001okx

Binding Structure of Elastase Inhibitor Scyptolin A

• PDB DOI: https://doi.org/10.2210/pdb1OKX/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa, Scytonema hofmannii
• Mutation(s): No 


• Deposited: 2003-07-31 Released: 2003-10-24 
• Deposition Author(s): Matern, U., Schleberger, C., Jelakovic, S., Weckesser, J., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Binding Structure of Elastase Inhibitor Scyptolin A

Matern, U., Schleberger, C., Jelakovic, S., Weckesser, J., Schulz, G.E.

(2003) Chem Biol 10: 997

• PubMed: 14583266 
• DOI: https://doi.org/10.1016/j.chembiol.2003.10.001
• Primary Citation Related Structures: 
  1OKX


• PubMed Abstract: 
  

  Natural bioactive compounds are of general interest to pharmaceutical research because they may be used as leads in drug development campaigns. Among them, scyptolin A and B from Scytonema hofmanni PCC 7110 are known to inhibit porcine pancreatic elastase, which in turn resembles the attractive drug target neutrophil elastase. The crystal structure of scyptolin A as bound to pancreatic elastase was solved at 2.8 A resolution. The inhibitor occupies the most prominent subsites S1 through S4 of the elastase and prevents a hydrolytic attack by covering the active center with its rigid ring structure. The observed binding structure may help to design potent elastase inhibitors.

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Organizational Affiliation: 
• Institut für Biologie II, Mikrobiologie, Albert-Ludwigs-Universität, Schänzlestrasse 1, D-79104 Freiburg im Breisgau, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 53.83 kDa 
• Atom Count: 3,885 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELASTASE 1	A, B	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SCYPTOLIN A	C, D	8	Scytonema hofmannii	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000187	C, D	SCYPTOLIN A	Polypeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.89	α = 90
b = 155.89	β = 90
c = 91.03	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-24 
Deposition Author(s): Matern, U., Schleberger, C., Jelakovic, S., Weckesser, J., Schulz, G.E.

Revision History  

• Version 1.0: 2003-10-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2018-06-13
  Changes: Data collection, Structure summary
• Version 1.4: 2019-07-31
  Changes: Advisory, Data collection, Derived calculations
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description