9xhr

Crystal Structure of Human Cathepsin B with a D-peptide substrate

Method: X-RAY DIFFRACTION D_max: 57.0 Å Quality: GOOD

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

Cathepsin B

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 79–333	Mutation：S115A	ACE-DAR-DLY-DTY-DTY-GLY-0QE × 1	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

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 9XHR	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
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	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
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	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
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	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
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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xhr
Deposition date deposition_date	2025-11-02
最后修订 last_revision	2026-05-06
Structure title title	Crystal Structure of Human Cathepsin B with a D-peptide substrate
Keywords keywords	complex, D-peptide substrate, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.09 Å
Radius of gyration Rg (electron density) rg_electron	17.22 Å
Forward intensity I(0) i0	27838600.00
Molecular weight molecular_weight	26739.0 kDa
Excluded volume excluded_volume	25624 Å³
Envelope volume envelope_volume	39218 Å³
Hydration-shell volume shell_volume	18585 Å³
Envelope diameter envelope_diameter	57.3 Å
Shell Rg shell_rg	23.85 Å
Envelope Rg envelope_rg	17.63 Å
Shape Rg shape_rg	17.19 Å
Total Rg total_rg	17.96 Å
Total atoms total_atoms	2011
Residues n_residues	256
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	57.0 Å
Rg (real space) rg_real	17.96 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	2.7840e+07
I(0) uncertainty (real space) i0_real_error	2.7340e+05
Rg (reciprocal space) rg_reciprocal	17.98 Å
I(0) (reciprocal space) i0_reciprocal	27840000.0000
Solution quality estimate total_estimate	0.8920
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.174
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5377000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cathepsin B
Molecular weight formula_weight	27956.2 kDa
EC 编号 ec_number	3.4.22.1
Mutation mutation	S115A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2272

KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGARPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector BsrGI-MCS-pcDNA3.1

Entity 2 Entity 2 polymer

Description description	ACE-DAR-DLY-DTY-DTY-GLY-0QE
Molecular weight formula_weight	745.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(D)
Chain IDs strand_id	C

XRKYYGX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

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8. Citations (1)

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Unit-cell length a length_a	31.098 Å
Unit-cell length b length_b	81.331 Å
Unit-cell length c length_c	94.219 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.800 Å
R factor r_factor	0.1479
R_work r_work	0.1467
R_free r_free	0.1697

fit	/app/data/saxs_computation/xh/9xhr/9xhr.fit
pddf	/app/data/pr_computation/xh/9xhr/9xhr.pr.out
profile	/app/data/saxs_computation/xh/9xhr/9xhr.dat

Crystal Structure of Human Cathepsin B with a D-peptide substrate

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

Cathepsin B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)