7RNC | pdb_00007rnc

Crystal structure of caspase-3 with inhibitor Ac-VDVVD-CHO

• PDB DOI: https://doi.org/10.2210/pdb7RNC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-29 Released: 2022-06-15 
• Deposition Author(s): McCue, W., Finzel, B.C.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structural Studies to Enable Drug Discovery

McCue, W.

(2021) Thesis 

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: 55.76 kDa 
• Atom Count: 4,038 
• Modeled Residue Count: 478 
• Deposited Residue Count: 484 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3 subunit p17	A, C	141	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 subunit p12	B, D	95	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
Ac-VDVVD-CHO	E [auth F], F [auth G]	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ASA	E [auth F], F [auth G]	L-PEPTIDE LINKING	C4 H7 N O3		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.248	α = 90
b = 85.221	β = 90
c = 97.621	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
PHASER	phasing
AutoProcess	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): McCue, W., Finzel, B.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5R01AG062199-03

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 2.0: 2023-06-28
  Changes: Advisory, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-07-05
  Changes: Database references
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 3.0: 2024-02-07
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 3.1: 2024-11-20
  Changes: Structure summary