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1gmy

Cathepsin B complexed with dipeptidyl nitrile inhibitor

Method: X-RAY DIFFRACTION Dmax: 91.4 Å Quality: EXCELLENT
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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 79–339 Fragment：PROTEASE DOMAIN, RESIDUES 80-333 AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.50 Resolution 1.90 Å R-free 0.199
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 79–339 Fragment：PROTEASE DOMAIN, RESIDUES 80-333 AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.50 Resolution 1.90 Å R-free 0.199
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 79–339 Fragment：PROTEASE DOMAIN, RESIDUES 80-333 AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.50 Resolution 1.90 Å R-free 0.199

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 1GMY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CSB Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors Deposited 1994-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 80–126（47 aa）
Chain B 129–333（205 aa）
Not recorded EP0 N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1CSB Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors Deposited 1994-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 80–126（47 aa）
Chain E 129–333（205 aa）
Not recorded EP0 N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1HUC THE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER CATHEPSIN B: THE STRUCTURAL BASIS FOR ITS SPECIFICITY Deposited 1993-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 80–126（47 aa）
Chain B 129–333（205 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1HUC THE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER CATHEPSIN B: THE STRUCTURAL BASIS FOR ITS SPECIFICITY Deposited 1993-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 80–126（47 aa）
Chain D 129–333（205 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1PBH CRYSTAL STRUCTURE OF HUMAN RECOMBINANT PROCATHEPSIN B AT 3.2 ANGSTROM RESOLUTION Deposited 1997-02-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–333（316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 6000, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.3
Resolution 3.20 Å R-free 0.252
2IPP Crystal Structure of the tetragonal form of human liver cathepsin B Deposited 2006-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 80–126（47 aa） Fragment：light chain, residues 80-126
Chain B 129–333（205 aa） Fragment：heavy chain, residues 129-333
Not recorded PYS 2-PYRIDINETHIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.15 Å
2PBH CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION Deposited 1997-02-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–333（316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 700 MM TRIS, PH 7.2
Resolution 3.30 Å R-free 0.269
3AI8 Cathepsin B in complex with the nitroxoline Deposited 2010-05-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 78–333（256 aa）
Not recorded HNQ 5-nitroquinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.1M citric acid, 21% PEG6000, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.11 Å R-free 0.244
3AI8 Cathepsin B in complex with the nitroxoline Deposited 2010-05-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 78–333（256 aa）
Not recorded HNQ 5-nitroquinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.1M citric acid, 21% PEG6000, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.11 Å R-free 0.244
3CBJ Chagasin-Cathepsin B complex Deposited 2008-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 74–339（266 aa）
Mutation：C29A, H110A, S115A PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium dihydrogen phosphate, 20% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.210
3CBJ Chagasin-Cathepsin B complex Deposited 2008-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 74–339（266 aa）
Mutation：C29A, H110A, S115A PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium dihydrogen phosphate, 20% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.210
3CBK chagasin-cathepsin B Deposited 2008-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 74–339（266 aa）
Mutation：C29A, H110A, S115A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.14M ammonium fluoride, 14% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.67 Å R-free 0.242
3K9M Cathepsin B in complex with stefin A Deposited 2009-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 80–333（254 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.250
3K9M Cathepsin B in complex with stefin A Deposited 2009-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 80–333（254 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.250
3PBH REFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM RESOLUTION Deposited 1997-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–333（316 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.72；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, PH 5.72
Resolution 2.50 Å R-free 0.234
5MBL Cathepsin B in complex with DARPin 81 Deposited 2016-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 78–333（256 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；292 K；buffer: 50mM Tris/HCl, 300mM NaCl, 0.05% Tween-20 precipitant: 0.1M MES, 1.8M NH4SO4
Resolution 1.81 Å R-free 0.193
5MBM Cathepsin B in complex with DARPin 8h6 Deposited 2016-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 78–333（256 aa） Fragment：UNP residues 78-333
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0,1 M Na-citrate 15% PEG6000
Resolution 2.76 Å R-free 0.281
5MBM Cathepsin B in complex with DARPin 8h6 Deposited 2016-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 78–333（256 aa） Fragment：UNP residues 78-333
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0,1 M Na-citrate 15% PEG6000
Resolution 2.76 Å R-free 0.281
6AY2 Structure of CathB with covalently linked Compound 28 Deposited 2017-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 79–333（255 aa）
Not recorded C1G N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；as published
Resolution 1.60 Å R-free 0.176
6AY2 Structure of CathB with covalently linked Compound 28 Deposited 2017-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 79–333（255 aa）
Not recorded C1G N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；as published
Resolution 1.60 Å R-free 0.176
8B4T Human cathepsin B in complex with the carbamate inhibitor 7 Deposited 2022-09-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 79–333（255 aa）
Mutation：S115A P9F (2S)-2-[[(2S)-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Sodium Acetate pH 5.5, 20% PEG 2000 MME
Resolution 1.45 Å R-free 0.208
8B5F Human cathepsin B in complex with the carbamate inhibitor 31 Deposited 2022-09-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 79–333（255 aa）
Mutation：S115A P9U (2S)-2-[[(2S)-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 MME
Resolution 1.70 Å R-free 0.205
8HE9 Crystal structure of CTSB in complex with K777 Deposited 2022-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 79–333（255 aa）
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
8HEI Crystal structure of CTSB in complex with E64d Deposited 2022-11-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–333（257 aa）
Not recorded E6D ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.55 Å R-free 0.173
8HEN Crystal structure of CTSB in complex with 212-148 Deposited 2022-11-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 77–333（257 aa）
Not recorded GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 L4F 2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Magnesium chloride hexahydrate, 0.1 M NaAc pH 5.2, 28% w/v PEG 3350
Resolution 1.95 Å R-free 0.232
9VA8 Crystal Structure of Human Cathepsin B with a L-peptide substrate Deposited 2025-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 80–333（254 aa）
Mutation：S115A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
Resolution 1.50 Å R-free 0.209
9XHR Crystal Structure of Human Cathepsin B with a D-peptide substrate Deposited 2025-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 79–333（255 aa）
Mutation：S115A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M bicine, 20% PEG 10K
Resolution 1.50 Å R-free 0.170

20 other PDB entries and 27 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 1–261； UniProt 79–339 Author chain B； PDBConstruct 1–261； UniProt 79–339 Author chain C； PDBConstruct 1–261； UniProt 79–339

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 1gmy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1gmy
Deposition date deposition_date2001-09-25
Structure title titleCathepsin B complexed with dipeptidyl nitrile inhibitor
Keywords keywords;HYDROLASE/INHIBITOR, COMPLEX (HYDROLASE-INHIBITOR), COVALENT COMPLEX, PROTEASE, CATHEPSIN B, HYDROLASE, THIOL PROTEASE, HYDROLASE-INHIBITOR complex ;; 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_guinier29.31 Å
Radius of gyration Rg (electron density) rg_electron28.72 Å
Forward intensity I(0) i0122867000.00
Molecular weight molecular_weight84273.0 kDa
Excluded volume excluded_volume103620 ų
Envelope volume envelope_volume124630 ų
Hydration-shell volume shell_volume35946 ų
Envelope diameter envelope_diameter97.3 Å
Shell Rg shell_rg36.17 Å
Envelope Rg envelope_rg28.49 Å
Shape Rg shape_rg28.71 Å
Total Rg total_rg29.40 Å
Total atoms total_atoms5923
Residues n_residues760
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 dmax91.4 Å
Rg (real space) rg_real29.23 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.2290e+08
I(0) uncertainty (real space) i0_real_error1.7600e+06
Rg (reciprocal space) rg_reciprocal29.27 Å
I(0) (reciprocal space) i0_reciprocal122900000.0000
Solution quality estimate total_estimate0.9080
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.1 Å
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.582
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha26210000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1gmya_
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_idd1gmyb_
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_idd1gmyc_
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 (3 domains)

Domain ID domain_id1gmyA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1gmyB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1gmyC00
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)