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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of human caspase-7 soaked with allosteric inhibitor

Vance, N.R., Gakhar, L., Spies, M.A.

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55210
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8YJ Query on 8YJ Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid C₁₅ H₁₁ Cl O₃ S SWPTTWQFPBNDMV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.