2XZT

Caspase-3 in Complex with DARPin-3.4_I78S

• PDB DOI: https://doi.org/10.2210/pdb2XZT/pdb

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


• Deposited: 2010-11-29 Released: 2011-12-14 
• Deposition Author(s): Barandun, J., Schroeder, T., Mittl, P., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Caspase-3 in Complex with Darpin-3.4_I78S

Schroeder, T., Barandun, J., Grutter, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.2 kDa 
• Atom Count: 5,800 
• Modelled Residue Count: 709 
• Deposited Residue Count: 806 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASPASE-3	A, C	149	Homo sapiens	Mutation(s): 0  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, D	118	Homo sapiens	Mutation(s): 0  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
DARPIN-3.4_I78S	E [auth G], F [auth H]	136	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	G [auth A], H [auth C], I [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, C	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98	α = 90
b = 98	β = 90
c = 193.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Barandun, J., Schroeder, T., Mittl, P., Grutter, M.G.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description