3D6H

Crystal structure of human caspase-1 with a naturally-occurring Asn263->Ser substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

• PDB DOI: https://doi.org/10.2210/pdb3D6H/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-19 Released: 2010-03-02 
• Deposition Author(s): Rosen-Wolff, A., Roesler, J., Romanowski, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Mutated, structurally altered caspase-1 with decreased enzymatic and increased RIP2-meditated inflammatory activity leads to a new type of periodic fever (ICE fever).

Rosen-Wolff, A., Romanowski, M.J., Ritter, L., Flecks, S., Quoos, N., Gramatt, J., Petzold, C., Nguyen, H.D., Gahr, M., Roesler, J.

To be published.

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: 30.84 kDa 
• Atom Count: 2,246 
• Modelled Residue Count: 259 
• Deposited Residue Count: 273 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	A	179	Homo sapiens	Mutation(s): 1  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
PHAROS:  P29466 GTEx:  ENSG00000137752

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1 precursor	B	89	Homo sapiens	Mutation(s): 0  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
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: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.377	α = 90
b = 63.377	β = 90
c = 142.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Rosen-Wolff, A., Roesler, J., Romanowski, M.J.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary