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CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN

Method: X-RAY DIFFRACTION Dmax: 82.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cathepsin B

Rattus norvegicus

UniProt P00787

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 74–333 Chain B； UniProt 74–333 Mutation：S115A 0E6 amino{[(4S)-4-{[(benzyloxy)carbonyl]amino}-5-{[(2S)-1-(benzyloxy)-4-chloro-3-oxobutan-2-yl]amino}-5-oxopentyl]amino}met haniminium × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.90 Å

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 1THE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CPJ CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN Deposited 1995-07-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 74–333（260 aa）
Chain B 74–333（260 aa）
Mutation：S115A Mutation：S115A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1CTE CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN Deposited 1995-05-03 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 80–333（254 aa）
Chain B 80–333（254 aa）
Not recorded PYS 2-PYRIDINETHIOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1MIR RAT PROCATHEPSIN B Deposited 1996-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–339（322 aa）
Mutation：C29S, S115A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.270
1MIR RAT PROCATHEPSIN B Deposited 1996-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 18–339（322 aa）
Mutation：C29S, S115A No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.270

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CATB_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–260； UniProt 74–333 Author chain B； PDBConstruct 1–260； UniProt 74–333

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 1the

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1the
Deposition date deposition_date1995-09-15
Structure title titleCRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
Keywords keywordsTHIOL PROTEASE, Glycoprotein, Protease, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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_guinier23.87 Å
Radius of gyration Rg (electron density) rg_electron23.05 Å
Forward intensity I(0) i0101802000.00
Molecular weight molecular_weight52303.0 kDa
Excluded volume excluded_volume50110 ų
Envelope volume envelope_volume79711 ų
Hydration-shell volume shell_volume28259 ų
Envelope diameter envelope_diameter81.2 Å
Shell Rg shell_rg30.66 Å
Envelope Rg envelope_rg23.31 Å
Shape Rg shape_rg23.01 Å
Total Rg total_rg23.72 Å
Total atoms total_atoms3932
Residues n_residues506
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 dmax82.0 Å
Rg (real space) rg_real23.79 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real1.0180e+08
I(0) uncertainty (real space) i0_real_error1.5630e+06
Rg (reciprocal space) rg_reciprocal23.81 Å
I(0) (reciprocal space) i0_reciprocal101800000.0000
Solution quality estimate total_estimate0.8723
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.358
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20030000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1thea_
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_idd1theb_
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_id1theA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1theB00
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 (2)

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9. Files and Curves (10)