6PZP | pdb_00006pzp

Crystal structure of caspase-1 in complex with VX-765

• PDB DOI: https://doi.org/10.2210/pdb6PZP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-01 Released: 2020-08-05 
• Deposition Author(s): Yang, J., Liu, Z., Xiao, T.S.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of caspase-1 in complex with VX-765

Yang, J., Liu, Z., Xiao, T.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.61 kDa 
• Atom Count: 2,269 
• Modeled Residue Count: 262 
• Deposited Residue Count: 266 
• Unique protein chains: 2

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
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	B	88	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P7S (Subject of Investigation/LOI)	C [auth A]	N-(4-amino-3-chlorobenzene-1-carbonyl)-3-methyl-L-valyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-prolinamide C22 H29 Cl N4 O6 SOZONDBMOYWSRW-QANKJYHBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P7S	BindingDB:  6PZP	Ki: 0.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.605	α = 90
b = 63.605	β = 90
c = 162.107	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Yang, J., Liu, Z., Xiao, T.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM127609

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary