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1mir

RAT PROCATHEPSIN B

Method: X-RAY DIFFRACTION Dmax: 114.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROCATHEPSIN 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 18–339 Mutation：C29S, S115A No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.270
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 18–339 Mutation：C29S, S115A No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.270

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 1MIR 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
1THE CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN Deposited 1995-09-15 Different construct Different mutation/modification Different oligomeric state 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 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 conditions Resolution 1.90 Å

3 other PDB entries and 3 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 63–322； UniProt 18–339 Author chain B； PDBConstruct 63–322； UniProt 18–339

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 1mir

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1mir
Deposition date deposition_date1996-01-12
Structure title titleRAT PROCATHEPSIN B
Keywords keywordsHYDROLASE, THIOL PROTEASE, CYSTEINE PROTEASE; 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_guinier37.86 Å
Radius of gyration Rg (electron density) rg_electron38.01 Å
Forward intensity I(0) i078943800.00
Molecular weight molecular_weight69055.0 kDa
Excluded volume excluded_volume84895 ų
Envelope volume envelope_volume112810 ų
Hydration-shell volume shell_volume25234 ų
Envelope diameter envelope_diameter123.7 Å
Shell Rg shell_rg43.06 Å
Envelope Rg envelope_rg37.19 Å
Shape Rg shape_rg37.94 Å
Total Rg total_rg38.53 Å
Total atoms total_atoms5924
Residues n_residues626
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 dmax114.5 Å
Rg (real space) rg_real38.34 Å
Rg uncertainty (real space) rg_real_error1.22 Å
I(0) (real space) i0_real7.8940e+07
I(0) uncertainty (real space) i0_real_error1.4820e+06
Rg (reciprocal space) rg_reciprocal38.06 Å
I(0) (reciprocal space) i0_reciprocal78920000.0000
Solution quality estimate total_estimate0.6358
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.5 Å
Skewness Skewness skewness0.328
Kurtosis Kurtosis kurtosis-1.083
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13450000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.314; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.311; Smooth: 0.010
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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_idd1mira_
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_idd1mirb_
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_id1mirA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1mirB00
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)