8he9

Crystal structure of CTSB in complex with K777

Method: X-RAY DIFFRACTION Dmax: 56.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cathepsin B

Homo sapiens

UniProt P07858

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 79–333 Not recorded 0IW Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide × 1 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;17.1 % v/v Polyethylene glycol 600, 50 mM MES pH 5.6, 8.6 % w/v Polyethylene glycol 4,000 Resolution 1.55 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

20 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CATB_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–255; UniProt 79–333

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8he9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8he9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8he9
Deposition date deposition_date2022-11-07
Structure title titleCrystal structure of CTSB in complex with K777
Keywords keywordsinhibitor, antiviral, protease, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-INHIBITOR complex; ANTIVIRAL PROTEIN/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.93
Radius of gyration Rg (electron density) rg_electron17.03
Forward intensity I(0) i027365000.00
Molecular weight molecular_weight26485.0 kDa
Excluded volume excluded_volume25398 ų
Envelope volume envelope_volume38302 ų
Hydration-shell volume shell_volume18352 ų
Envelope diameter envelope_diameter56.7
Shell Rg shell_rg23.66
Envelope Rg envelope_rg17.41
Shape Rg shape_rg17.00
Total Rg total_rg17.80
Total atoms total_atoms1988
Residues n_residues253
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax56.5
Rg (real space) rg_real17.81
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real2.7360e+07
I(0) uncertainty (real space) i0_real_error2.8890e+05
Rg (reciprocal space) rg_reciprocal17.82
I(0) (reciprocal space) i0_reciprocal27370000.0000
Solution quality estimate total_estimate0.8943
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9
Skewness Skewness skewness0.166
Kurtosis Kurtosis kurtosis-0.404
Angular range angular_range— – 0.4450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5601000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)