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1deu

CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE

Method: X-RAY DIFFRACTION Dmax: 150.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROCATHEPSIN X

OrganismNot specified

UniProt Q9UBR2

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 27–303 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；292 K；300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 1.70 Å R-free 0.215
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 27–303 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；292 K；300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 1.70 Å R-free 0.215
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 27–303 Chain B； UniProt 27–303 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；292 K；300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 1.70 Å R-free 0.215

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.

Other PDB Difference from Current Entry 1DEU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EF7 CRYSTAL STRUCTURE OF HUMAN CATHEPSIN X Deposited 2000-02-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 52–293（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, 2-propanol, Na-HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.67 Å R-free 0.226
1EF7 CRYSTAL STRUCTURE OF HUMAN CATHEPSIN X Deposited 2000-02-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 52–293（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, 2-propanol, Na-HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.67 Å R-free 0.226
1EF7 CRYSTAL STRUCTURE OF HUMAN CATHEPSIN X Deposited 2000-02-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 52–293（242 aa）
Chain B 52–293（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, 2-propanol, Na-HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.67 Å R-free 0.226

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CATZ_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–277； UniProt 27–303 Author chain B； PDBConstruct 1–277； UniProt 27–303

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 1deu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1deu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1deu
Deposition date deposition_date1999-11-15
Structure title titleCRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE
Keywords keywordsCYSTEINE PROTEASE, PROCATHEPSIN X, PROREGION, PROSEGMENT, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.38 Å
Radius of gyration Rg (electron density) rg_electron47.59 Å
Forward intensity I(0) i058766400.00
Molecular weight molecular_weight59620.0 kDa
Excluded volume excluded_volume72863 ų
Envelope volume envelope_volume123680 ų
Hydration-shell volume shell_volume21646 ų
Envelope diameter envelope_diameter131.2 Å
Shell Rg shell_rg54.95 Å
Envelope Rg envelope_rg43.41 Å
Shape Rg shape_rg47.57 Å
Total Rg total_rg47.96 Å
Total atoms total_atoms4193
Residues n_residues536
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax150.6 Å
Rg (real space) rg_real47.91 Å
Rg uncertainty (real space) rg_real_error1.99 Å
I(0) (real space) i0_real5.8770e+07
I(0) uncertainty (real space) i0_real_error1.1400e+06
Rg (reciprocal space) rg_reciprocal47.39 Å
I(0) (reciprocal space) i0_reciprocal58730000.0000
Solution quality estimate total_estimate0.5416
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.8 Å
Skewness Skewness skewness0.054
Kurtosis Kurtosis kurtosis-1.645
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1196000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.037; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1deua_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like
Domain ID domain_idd1deub_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.1 — Papain-like

CATH v4.4 (2 domains)

Domain ID domain_id1deuA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1deuB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
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8. Citations (1)

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9. Files and Curves (10)