6X8I

Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct

• PDB DOI: https://doi.org/10.2210/pdb6X8I/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-01 Released: 2021-06-02 
• Deposition Author(s): Solania, A., Xu, J.H., Wolan, D.W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct

Solania, A., Xu, J.H., Wolan, D.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

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

Macromolecule Content

• Total Structure Weight: 66.6 kDa 
• Atom Count: 4,178 
• Modelled Residue Count: 477 
• Deposited Residue Count: 580 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	A, C [auth B]	175	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
PHAROS:  P42574 GTEx:  ENSG00000164305

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	B [auth C], D	110	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
PHAROS:  P42574 GTEx:  ENSG00000164305

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ketomethylene inhibitor	E, F	5	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.652	α = 90
b = 85.007	β = 90
c = 97.145	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Solania, A., Xu, J.H., Wolan, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R21AI112796
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM118382

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Advisory, Author supporting evidence, Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations