Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
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,PQS (software)

Macromolecule Content

• Total Structure Weight: 30.60 kDa 
• Atom Count: 2294 
• Residue Count: 261 
• Unique protein chains: 3

2HBQ

Crystal structure of wildtype human caspase-1 in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

• DOI: 10.2210/pdb2HBQ/pdb
• Entry: 2HBQ supersedes: 2FQR

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


• Deposited: 2006-06-14 Released: 2006-06-27 
• Deposition Author(s): Scheer, J.M., Wells, J.A., Romanowski, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

A Common Allosteric Site and Mechanism in Caspases

Scheer, J.M., Romanowski, M.J., Wells, J.A.

(2006) Proc Natl Acad Sci U S A 103: 7595-7600

• PubMed: 16682620 
• DOI: 10.1073/pnas.0602571103
• Primary Citation of Related Structures:  
  2HBR, 2HBQ, 2HBZ, 2HBY, 2FQQ, 2H48


• PubMed Abstract: 
  

We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, CA 94143, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	A	178	Homo sapiens	Mutation(s): 0  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
NIH Common Fund Data Resources
PHAROS:  P29466 GTEx:  ENSG00000137752

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	B	88	Homo sapiens	Mutation(s): 0  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
NIH Common Fund Data Resources
PHAROS:  P29466 GTEx:  ENSG00000137752

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide	C	5	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000338	C	N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.301	α = 90
b = 63.301	β = 90
c = 161.681	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
d*TREK	data reduction
AMoRE	phasing
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-14 
• Released Date: 2006-06-27 
Deposition Author(s): Scheer, J.M., Wells, J.A., Romanowski, M.J.
• This entry supersedes: 2FQR

Revision History 

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other