Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 63.59 kDa 
• Atom Count: 4134 
• Residue Count: 479 
• Unique protein chains: 4

2QL9

Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO

• DOI: 10.2210/pdb2QL9/pdb

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


• Deposited: 2007-07-12 Released: 2007-08-28 
• Deposition Author(s): Agniswamy, J., Fang, B., Weber, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 

Literature

Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis.

Agniswamy, J., Fang, B., Weber, I.T.

(2007) FEBS J 274: 4752-4765

• PubMed: 17697120 
• DOI: 10.1111/j.1742-4658.2007.05994.x
• Primary Citation of Related Structures:  
  2QLB, 2QLJ, 2QLF, 2QL9, 2QL7, 2QL5


• PubMed Abstract: 
  

Many protein substrates of caspases are cleaved at noncanonical sites in comparison to the recognition motifs reported for the three caspase subgroups. To provide insight into the specificity and aid in the design of drugs to control cell death, crystal structures of caspase-7 were determined in complexes with six peptide analogs (Ac-DMQD-Cho, Ac-DQMD-Cho, Ac-DNLD-Cho, Ac-IEPD-Cho, Ac-ESMD-Cho, Ac-WEHD-Cho) that span the major recognition motifs of the three subgroups. The crystal structures show that the S2 pocket of caspase-7 can accommodate diverse residues. Glu is not required at the P3 position because Ac-DMQD-Cho, Ac-DQMD-Cho and Ac-DNLD-Cho with varied P3 residues are almost as potent as the canonical Ac-DEVD-Cho. P4 Asp was present in the better inhibitors of caspase-7. However, the S4 pocket of executioner caspase-7 has alternate regions for binding of small branched aliphatic or polar residues similar to those of initiator caspase-8. The observed plasticity of the caspase subsites agrees very well with the reported cleavage of many proteins at noncanonical sites. The results imply that factors other than the P4-P1 sequence, such as exosites, contribute to the in vivo substrate specificity of caspases. The novel peptide binding site identified on the molecular surface of the current structures is suggested to be an exosite of caspase-7. These results should be considered in the design of selective small molecule inhibitors of this pharmacologically important protease.

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Organizational Affiliation: 

Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30302, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	A, C	173	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	B, D	97	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor AC-DQMD-CHO	E, F	5	N/A	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE QGHGE	G	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000284	E, F	AC-DQMD-CHO	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.197 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.158	α = 90
b = 87.158	β = 90
c = 187.416	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-12 
• Released Date: 2007-08-28 
Deposition Author(s): Agniswamy, J., Fang, B., Weber, I.

Revision History 

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other