5V6Z | pdb_00005v6z

Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb5V6Z/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-17 Released: 2018-03-21 
• Deposition Author(s): Vance, N.R., Gakhar, L., Spies, M.A.
• Funding Organization(s): University of Iowa College of Pharmacy

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human caspase-7 soaked with allosteric inhibitor

Vance, N.R., Gakhar, L., Spies, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.95 kDa 
• Atom Count: 3,175 
• Modelled Residue Count: 411 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	A, B	303	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
PHAROS:  P55210 GTEx:  ENSG00000165806

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8YJ	C [auth B]	2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid C15 H11 Cl O3 S SWPTTWQFPBNDMV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.344	α = 90
b = 89.344	β = 90
c = 184.898	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Vance, N.R., Gakhar, L., Spies, M.A.

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Funding Organization	Location	Grant Number
University of Iowa College of Pharmacy	United States	--

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary