7X79 | pdb_00007x79

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

• PDB DOI: https://doi.org/10.2210/pdb7X79/pdb

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


• Deposited: 2022-03-09 Released: 2023-06-14 
• 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: 1.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

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

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: 82.7 kDa 
• Atom Count: 2,934 
• Modeled Residue Count: 322 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
89K (Subject of Investigation/LOI)	B [auth A]	N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide C34 H42 N4 O6 QBWBVQMSMXVSSF-YRUYCOJQSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
H2S	C [auth A]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.203	α = 90
b = 64.07	β = 90
c = 99.576	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: 2023-06-14 
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	813300237

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary