8GX3 | pdb_00008gx3

The crystal structure of human Calpain-1 protease core in complex with 14c

• PDB DOI: https://doi.org/10.2210/pdb8GX3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-18 Released: 2023-09-20 
• Deposition Author(s): Zhao, Y., Zhao, J., Shao, M., Yang, H., Rao, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

The crystal structure of human Calpain-1 protease core in complex with 14c

Zhao, Y., Zhao, J., Shao, M., Yang, H., Rao, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.62 kDa 
• Atom Count: 2,951 
• Modeled Residue Count: 327 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain-1 catalytic subunit	A	714	Homo sapiens	Mutation(s): 0  Gene Names: CAPN1, CANPL1, PIG30 EC: 3.4.22.52
UniProt & NIH Common Fund Data Resources
Find proteins for P07384 (Homo sapiens) Explore P07384  Go to UniProtKB:  P07384
PHAROS:  P07384 GTEx:  ENSG00000014216

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KJ0 (Subject of Investigation/LOI)	B [auth A]	N-[(2S)-3-cyclohexyl-1-[[(2S,3S)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide C30 H40 N4 O6 FLHCDUBGBDAQOK-SZBRSHHCSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.329	α = 90
b = 64.14	β = 90
c = 99.782	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Zhao, Y., Zhao, J., Shao, M., Yang, H., Rao, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200131

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary