2IOT | pdb_00002iot

Clavulanic Acid bound to Elastase

• PDB DOI: https://doi.org/10.2210/pdb2IOT/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2006-10-10 Released: 2008-04-08 
• Deposition Author(s): Farady, C., Navia, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.208 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Elastase Inhibition by Clavulanic Acid, and Inhibitor of Bacterial b-lactamases: Mechanistic and Structural Studies

Farady, C., Ali, J.A., Navia, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.16 kDa 
• Atom Count: 2,183 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL5	C [auth A]	N-(3-OXOPROPYL)GLYCINE C5 H9 N O3 KCNYJRBIWGISEE-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.208 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.7	α = 90
b = 57.7	β = 90
c = 74.3	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Farady, C., Navia, M.A.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary