9VA8 | pdb_00009va8

Crystal Structure of Human Cathepsin B with a L-peptide substrate

PDB DOI: https://doi.org/10.2210/pdb9VA8/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Mammalian expression vector BsrGI-MCS-pcDNA3.1
Mutation(s): Yes

Deposited: 2025-06-03 Released: 2026-05-06
Deposition Author(s): Li, M., Li, T., Chen, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9VA8

This is version 1.0 of the entry. See complete history.

Literature

Transcending stereochemical boundaries: ambidextrous cleavage of D- and L-peptide enantiomers by natural eukaryotic proteases

Li, M., Chen, K., Zhang, W., Han, J., Guo, M., Zhu, X., Zheng, J., Li, T., Dang, B.

(2026) Vita

DOI: https://doi.org/10.15302/vita.2026.03.0022

Macromolecule Content

Total Structure Weight: 28.24 kDa
Atom Count: 2,189
Modeled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A	254	Homo sapiens	Mutation(s): 1 Gene Names: CTSB, CPSB EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858 Go to UniProtKB: P07858
PHAROS: P07858 GTEx: ENSG00000164733
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07858
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)YY(F3V)	B [auth C]	4	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.617	α = 90
b = 75.096	β = 90
c = 97.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing
HKL-3000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.