1stf

THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION

Method: X-RAY DIFFRACTION D_max: 70.8 Å Quality: GOOD

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

PAPAIN

Carica papaya

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 E； UniProt 134–345	Non-standard monomer：Yes (specific site not provided by mmCIF)	STEFIN B (CYSTATIN B) × 1 （P04080）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.37 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 1STF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BP4 USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES. Deposited 1998-08-12	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 134–345（212 aa） Fragment：NON	Not recorded	ALD N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.20 Å R-free 0.240
1BQI USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES. Deposited 1998-08-16	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 134–345（212 aa）	Not recorded	SBA CARBOBENZYLOXY-(L)-LEUCINYL-(L)LEUCINYL METHOXYMETHYLKETONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.50 Å R-free 0.306
1CVZ CRYSTAL STRUCTURE ANALYSIS OF PAPAIN WITH CLIK148(CATHEPSIN L SPECIFIC INHIBITOR) Deposited 1999-08-24	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 134–345（212 aa） Fragment：RESIDUES 134-345	Not recorded	C48 N1-(1-DIMETHYLCARBAMOYL-2-PHENYL-ETHYL)-2-OXO-N4-(2-PYRIDIN-2-YL-ETHYL)-SUCCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；277 K；sodium chloride, methanol, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.70 Å R-free 0.214
1KHP Monoclinic form of papain/ZLFG-DAM covalent complex Deposited 2001-11-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa） Fragment：Papain, Residues 134-345	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；292 K；68% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.229
1KHQ ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX Deposited 2001-11-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa） Fragment：Papain, Residues 134-345	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；292 K；72% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.60 Å R-free 0.169
1PAD Binding of chloromethyl ketone substrate analogues to crystalline papain Deposited 1976-11-01	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1PE6 REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION Deposited 1991-05-14	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 134–345（212 aa）	Not recorded	E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1 MOH METHANOL × 14	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1PIP CRYSTAL STRUCTURE OF PAPAIN-SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE COMPLEX AT 1.7 ANGSTROMS RESOLUTION: NONCOVALENT BINDING MODE OF A COMMON SEQUENCE OF ENDOGENOUS THIOL PROTEASE INHIBITORS Deposited 1992-10-03	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1POP X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A PAPAIN-LEUPEPTIN COMPLEX Deposited 1993-06-24	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Not recorded	MOH METHANOL × 24	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1PPD RESTRAINED LEAST-SQUARES REFINEMENT OF THE SULFHYDRYL PROTEASE PAPAIN TO 2.0 ANGSTROMS Deposited 1984-11-06	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 134–345（212 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1PPN STRUCTURE OF MONOCLINIC PAPAIN AT 1.60 ANGSTROMS RESOLUTION Deposited 1991-10-25	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 134–345（212 aa）	Not recorded	UNL UNKNOWN LIGAND × 1 MOH METHANOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1PPP CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES Deposited 1993-03-17	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 134–345（212 aa）	Not recorded	E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1 MOH METHANOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
2CIO The high resolution x-ray structure of papain complexed with fragments of the Trypanosoma brucei cysteine protease inhibitor ICP. Deposited 2006-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；50% ETHANOL, 0.01M NA ACETATE, pH 7.50	Resolution 1.50 Å R-free 0.225
2PAD BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO CRYSTALLINE PAPAIN Deposited 1976-11-01	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 134–345（212 aa）	Not recorded	CYS CYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
3E1Z Crystal structure of the parasite protesase inhibitor chagasin in complex with papain Deposited 2008-08-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 134–345（212 aa）	Not recorded	ZN ZINC ION × 1 FMT FORMIC ACID × 10 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2.0M ammonium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.86 Å R-free 0.208
3IMA Complex structure of tarocystatin and papain Deposited 2009-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa） Fragment：Papain domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；30% PEG MME 2000, 0.1M Sodium Acetate trihydrate pH 4.6, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.03 Å R-free 0.233
3IMA Complex structure of tarocystatin and papain Deposited 2009-08-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 134–345（212 aa） Fragment：Papain domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；30% PEG MME 2000, 0.1M Sodium Acetate trihydrate pH 4.6, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.03 Å R-free 0.233
3LFY CTD of Tarocystatin in complex with papain Deposited 2010-01-19	Different construct 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 134–345（212 aa） Fragment：Papain DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SER SERINE × 1 ASN ASPARAGINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.267
3LFY CTD of Tarocystatin in complex with papain Deposited 2010-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 134–345（212 aa） Fragment：Papain DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	SER SERINE × 1 ASN ASPARAGINE × 1 GLY GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.267
3TNX Structure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution Deposited 2011-09-02	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 27–345（319 aa） Fragment：UNP residues 27-345	Mutation：C132A, V139S, G143S, K281R	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；8.0% PEG 3350, 0.1M Na-acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.236
3TNX Structure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution Deposited 2011-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–345（319 aa） Fragment：UNP residues 27-345	Mutation：C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；8.0% PEG 3350, 0.1M Na-acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.236
3USV Structure of the precursor of a thermostable variant of papain at 3.8 A resolution from a crystal soaked at pH 4 Deposited 2011-11-24	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 27–345（319 aa） Fragment：UNP residues 27-345	Mutation：C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；CS37 of Hampton Research, soaked overnight in NaOAc buffer pH 4.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.80 Å R-free 0.408
3USV Structure of the precursor of a thermostable variant of papain at 3.8 A resolution from a crystal soaked at pH 4 Deposited 2011-11-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–345（319 aa） Fragment：UNP residues 27-345	Mutation：C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；CS37 of Hampton Research, soaked overnight in NaOAc buffer pH 4.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.80 Å R-free 0.408
4PAD Binding of chloromethyl ketone substrate analogues to crystalline papain Deposited 1976-11-01	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 134–345（212 aa）	Not recorded	TCK N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
4QRG Crystal structure of I86L mutant of papain Deposited 2014-07-01	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 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：I86L, C132A, V139S, G143S, K281R	NA SODIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 2.50 Å R-free 0.223
4QRG Crystal structure of I86L mutant of papain Deposited 2014-07-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：I86L, C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 2.50 Å R-free 0.223
4QRV Crystal structure of I86F mutant of papain Deposited 2014-07-02	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 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：I86F, C132A, V139S, G143S, K281R	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 1.98 Å R-free 0.249
4QRV Crystal structure of I86F mutant of papain Deposited 2014-07-02	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 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：I86F, C132A, V139S, G143S, K281R	CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 1.98 Å R-free 0.249
4QRX Crystal structure of pro-papain mutant at pH 4.0 Deposited 2014-07-02	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 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 3.14 Å R-free 0.254
4QRX Crystal structure of pro-papain mutant at pH 4.0 Deposited 2014-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–345（319 aa） Fragment：UNP RESIDUES 27-345	Mutation：C132A, V139S, G143S, K281R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；298 K；8% PEG 4000, pH 7.5, hanging drop, temperature 298K	Resolution 3.14 Å R-free 0.254
5PAD BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO CRYSTALLINE PAPAIN Deposited 1976-11-01	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
6H8T Crystal structure of Papain modify by achiral Ru(II)complex Deposited 2018-08-03	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 134–345（212 aa）	Not recorded	ACT ACETATE ION × 3 CL CHLORIDE ION × 1 YXZ chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.7；277 K；35% PEG400, 50mM sodium acetate, 100mM lithium sulfate	Resolution 2.10 Å R-free 0.249
6H8T Crystal structure of Papain modify by achiral Ru(II)complex Deposited 2018-08-03	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 J 134–345（212 aa）	Not recorded	ACT ACETATE ION × 6 YXX chloro(1-{5-[di(pyridin-2-yl-kappaN)amino]pentyl}pyrrolidine-2,5-dione)ruthenium × 1 SO4 SULFATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.7；277 K；35% PEG400, 50mM sodium acetate, 100mM lithium sulfate	Resolution 2.10 Å R-free 0.249
6PAD Binding of chloromethyl ketone substrate analogues to crystalline papain Deposited 1976-11-01	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 134–345（212 aa）	Not recorded	0PC Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro-1-methyl-2-oxopropyl]-L-phenylalaninamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
6TCX Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis Deposited 2019-11-06	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 AAA 134–345（212 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 N1W (2~{R})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-3-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-(4-hydroxyphenyl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM HEPES pH 7.5 and 80% 2-Methyl-2,4-pentanediol (MPD)	Resolution 1.65 Å R-free 0.221
9CKT X-ray diffraction structure of papain co-crystallized with E-64 Deposited 2024-07-09	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 134–345（212 aa）	Not recorded	MOH METHANOL × 1 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；66% methanol (in sitting drop); 59% methanol, 889 mM NaCl (in reservoir).	Resolution 1.50 Å R-free 0.219
9CKW X-ray diffraction structure of papain co-crystallized with E-64D Deposited 2024-07-10	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 134–345（212 aa）	Not recorded	MOH METHANOL × 1 E6D ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；66% methanol (in sitting drop); 59% methanol, 889 mM NaCl (in reservoir).	Resolution 1.40 Å R-free 0.175
9CKY X-ray diffraction structure of papain co-crystallized with novel biosynthetic inhibitor amine-65 Deposited 2024-07-10	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 134–345（212 aa）	Not recorded	MOH METHANOL × 1 A1AXI (3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；66% methanol (in sitting drop); 59% methanol, 889 mM NaCl (in reservoir).	Resolution 1.40 Å R-free 0.199
9CLH X-ray diffraction structure of the apo form of papain Deposited 2024-07-11	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 134–345（212 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MOH METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；66% methanol (in sitting drop); 59% methanol, 889 mM NaCl (in reservoir).	Resolution 1.60 Å R-free 0.191
9EG7 X-ray diffraction structure of papain co-crystallized with E64-C Deposited 2024-11-20	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 134–345（212 aa）	Not recorded	E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；66% methanol (sitting well); 66% methanol, sodium chloride	Resolution 1.50 Å R-free 0.165
9N9D MicroED structure of papain co-crystallized with E-64C Deposited 2025-02-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å R-free 0.236
9NAE MicroED structure of papain co-crystallized with E-64 Deposited 2025-02-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å R-free 0.257
9NAG MicroED structure of the apo-form of papain Deposited 2025-02-12	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å R-free 0.248
9NAO MicroED structure of papain complexed with natural product E64-A65 Deposited 2025-02-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	A1AXI (3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å R-free 0.265
9NAR MicroED structure of papain microcrystals soaked with E-64 for 10 minutes Deposited 2025-02-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å R-free 0.206
9NAT X-ray diffraction structure of papain co-crystallized with leupeptin Deposited 2025-02-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–345（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；59% methanol, 889 mM NaCl in reservoir, 66% methanol in sitting well	Resolution 1.60 Å R-free 0.198
9NAX MicroED structure of the papain-E-64 complex from microcrystals soaked with crude biosynthetic reaction mixture Deposited 2025-02-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å R-free 0.247
9NAY MicroED structure of papain complexed with natural product E-64-A65 from microcrystals soaked in crude biosynthetic reaction mixture Deposited 2025-02-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	A1AXI (3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å R-free 0.228
9NB2 X-ray diffraction structure of papain soaked with E-64 Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl and 59% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.50 Å R-free 0.212
9NB4 Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with natural product E-64-A65 Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	A1AXI (3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 59% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.80 Å R-free 0.210
9NB7 Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with natural product E405 Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	A1BWT (3R)-4-({(2S)-1-[(5-acetamidopentyl)amino]-1-oxo-3-phenylpropan-2-yl}amino)-3-hydroxy-4-oxobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 58% methanol in reservoir. 66% methanol in sitting drop	Resolution 1.80 Å R-free 0.215
9NBF Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with E-64 Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 58% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.80 Å R-free 0.239
9NBJ Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with E-64C Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 58% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.80 Å R-free 0.210
9NBK Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with E-64D Deposited 2025-02-13	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 134–345（212 aa）	Not recorded	E6D ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 58% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.80 Å R-free 0.198
9NBN Serial synchrotron X-ray diffraction structure of papain microcrystals soaked with a mixture of E-64, E-64C, and E-64D Deposited 2025-02-14	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 134–345（212 aa）	Not recorded	A1BWS (3S)-4-{[(2S)-1-amino-4-methyl-1-oxopentan-2-yl]amino}-3-hydroxy-4-oxobutanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM NaCl, 58% methanol in reservoir. 66% methanol in sitting drop.	Resolution 1.80 Å R-free 0.238
9NBP MicroED structure of the papain-E-64 complex from microcrystals mixed on-grid with microarrayed ligand Deposited 2025-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å R-free 0.246
9NBQ MicroED structure of papain co-crystallized with E-64D Deposited 2025-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E6D ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å R-free 0.247
9NC1 MicroED structure of papain-E-64 complex from microcrystals soaked with protease inhibitor cocktail Deposited 2025-02-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å R-free 0.261
9NCA MicroED structure of microcrystals soaked with a mixture of E-64, E-64C, and E-64D Deposited 2025-02-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1 E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE × 1	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å R-free 0.276
9NCC Serial synchrotron X-ray diffraction structure of the apo form of papain Deposited 2025-02-15	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 134–345（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；889 mM sodium chloride, 59% methanol in reservoir, 66% methanol in sitting drop	Resolution 1.80 Å R-free 0.233
9PAP STRUCTURE OF PAPAIN REFINED AT 1.65 ANGSTROMS RESOLUTION Deposited 1986-03-31	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–345（212 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MOH METHANOL × 29	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å

53 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAPA1_CARPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–212； UniProt 134–345

STEFIN B (CYSTATIN B)

Homo sapiens

UniProt P04080

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 I； UniProt 1–98	Not recorded	PAPAIN × 1 （P00784）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.37 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1STF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OCT Stefin B (Cystatin B) tetramer Deposited 2006-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–98（98 aa） Chain B 1–98（98 aa）	Mutation：C3S, P79S Mutation：C3S, P79S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；30 % MPD, 0.1 M HEPES, 1.4-butanediol as additive, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.189
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 2 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 5 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 1 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 9 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 8 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 7 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 6 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 4 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 3 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 0 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYTB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–98； UniProt 1–98

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	1stf
Deposition date deposition_date	1993-04-21
Structure title title	THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION
Keywords keywords	HYDROLASE(SULFHYDRYL PROTEINASE); HYDROLASE(SULFHYDRYL PROTEINASE)
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	21.42 Å
Radius of gyration Rg (electron density) rg_electron	20.72 Å
Forward intensity I(0) i0	20968900.00
Molecular weight molecular_weight	34652.0 kDa
Excluded volume excluded_volume	43243 Å³
Envelope volume envelope_volume	49889 Å³
Hydration-shell volume shell_volume	20559 Å³
Envelope diameter envelope_diameter	73.2 Å
Shell Rg shell_rg	26.87 Å
Envelope Rg envelope_rg	21.11 Å
Shape Rg shape_rg	20.72 Å
Total Rg total_rg	21.50 Å
Total atoms total_atoms	2448
Residues n_residues	306
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	70.8 Å
Rg (real space) rg_real	21.44 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.0970e+07
I(0) uncertainty (real space) i0_real_error	2.7560e+05
Rg (reciprocal space) rg_reciprocal	21.44 Å
I(0) (reciprocal space) i0_reciprocal	20970000.0000
Solution quality estimate total_estimate	0.8067
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.407
Kurtosis Kurtosis kurtosis	-0.255
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7139000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

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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	PAPAIN
Molecular weight formula_weight	23507.4 kDa
EC 编号 ec_number	3.4.22.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	2590

IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN

来源 Source

来源生物 organism	Carica papaya
通用名 common_name	papaya
NCBI Class编号 ncbi_taxonomy_id	3649
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	STEFIN B (CYSTATIN B)
Molecular weight formula_weight	11173.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MMSGAPSATQPATAETQHIADQVRSQLEEKYNKKFPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHLRVFQSLPHENKPLTLSNYQTNKAKHDELTYF

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	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1stfe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1stfi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

CATH v4.4 (2 domains)

Domain ID domain_id	1stfE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1stfI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (3)

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Unit-cell length a length_a	67.000 Å
Unit-cell length b length_b	67.000 Å
Unit-cell length c length_c	169.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.370 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	—

fit	/app/data/saxs_computation/st/1stf/1stf.fit
pddf	/app/data/pr_computation/st/1stf/1stf.pr.out
profile	/app/data/saxs_computation/st/1stf/1stf.dat

THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION

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

PAPAIN

State in the Current Structure

Other States of the Same Protein in the Database

STEFIN B (CYSTATIN 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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)