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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 134–345 | Not recorded | UNL UNKNOWN LIGAND × 1 MOH METHANOL × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions | Resolution 1.60 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 1PPN | 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 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 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 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 oligomeric state 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, 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 oligomeric state 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, 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 oligomeric state 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 | 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 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 oligomeric state 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 | 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 oligomeric state 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 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 |
| 1PPP CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES Deposited 1993-03-17 | 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 |
| 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 Deposited 1993-04-21 | Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
134–345（212 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.37 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 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
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 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 oligomeric state 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 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
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 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 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 mutation/modification 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 mutation/modification 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 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 ligand/ion 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 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 | 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 ligand/ion 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 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 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 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：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 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 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 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 | 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 ligand/ion 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 oligomeric state 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 | 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 | 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 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 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 oligomeric state 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）
|
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 | 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 mutation/modification 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 | PAPA_CARPA |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–212； UniProt 134–345 |