3qgj

1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal

Method: X-RAY DIFFRACTION D_max: 82.2 Å Quality: GOOD

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

Alpha-lytic protease

OrganismNot specified

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 200–397	Fragment：residues 200-397	Ac-AlaAlaPro-Alanal peptide × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 4 TFA trifluoroacetic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；277 K；1.2M Li2SO4, 20mM Tris-SO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.192
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 200–397	Fragment：residues 200-397	Ac-AlaAlaPro-Alanal peptide × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 3 TFA trifluoroacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；277 K；1.2M Li2SO4, 20mM Tris-SO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.192
3	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 200–397 Chain C； UniProt 200–397	Fragment：residues 200-397	Ac-AlaAlaPro-Alanal peptide × 4 EDO 1,2-ETHANEDIOL × 10 SO4 SULFATE ION × 14 TFA trifluoroacetic acid × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；277 K；1.2M Li2SO4, 20mM Tris-SO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.192

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 3QGJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOQ PRO REGION C-TERMINUS: PROTEASE ACTIVE SITE INTERACTIONS ARE CRITICAL IN CATALYZING THE FOLDING OF ALPHA-LYTIC PROTEASE Deposited 1998-08-05	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 200–397（198 aa）	Mutation：V119I	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.10 Å R-free 0.236
1GBA ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY ALA Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1GBB Alpha-lytic protease with met 190 replaced by ALA AND GLY 216 replaced by ALA complex with METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1GBC ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-LEUCINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1GBD ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1GBE ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216L	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1GBF ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216L	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1GBH ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-LEUCINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216L	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1GBI ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A, G216L	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1GBJ ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1GBK ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.13 Å
1GBL ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-LEUCINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1GBM ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID Deposited 1995-09-06	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 200–397（198 aa）	Mutation：M190A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.28 Å
1P01 Serine protease mechanism. structure of an inhibitory complex oF ALPHA-LYTIC Protease and a tightly bound peptide boronic acid Deposited 1989-04-24	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 200–397（198 aa）	Not recorded	0EG N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1P02 STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1P03 STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1P04 STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.55 Å
1P05 STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1P06 STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.34 Å
1P09 STRUCTURAL PLASTICITY AS A DETERMINANT OF ENZYME SPECIFICITY. CREATING BROADLY SPECIFIC PROTEASES Deposited 1989-04-24	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 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1P10 STRUCTURAL PLASTICITY AS A DETERMINANT OF ENZYME SPECIFICITY. CREATING BROADLY SPECIFIC PROTEASES Deposited 1989-04-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
1P11 CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS Deposited 1990-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.93 Å
1P12 CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS Deposited 1990-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1QQ4 CRYSTAL STRUCTURE OF AN ALPHA-LYTIC PROTEASE MUTANT WITH ACCELERATED FOLDING KINETICS, R102H/G134S Deposited 1999-06-10	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 200–397（198 aa） Fragment：RESIDUES 1-198	Mutation：R102H,G134S	SO4 SULFATE ION × 5 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.14；298 K；lithium sulfate, tris-sulfate, pH 5.14, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.174
1QRW CRYSTAL STRUCTURE OF AN ALPHA-LYTIC PROTEASE MUTANT WITH ACCELERATED FOLDING KINETICS, R102H/G134S, PH 8 Deposited 1999-06-16	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 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN, RESIDUES 1-198	Mutation：R102H,G134S	SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；LITHIUM SULFATE, TRIS-SULFATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.181
1QRX CRYSTAL STRUCTURE OF WILD-TYPE ALPHA-LYTIC PROTEASE AT 1.6 A, PH 5.14 Deposited 1999-06-16	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 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN, RESIDUES 1-198	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.14；298 K；LITHIUM SULFATE, TRIS-SULFATE, pH 5.14, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.169
1SSX 0.83A resolution crystal structure of alpha-lytic protease at pH 8 Deposited 2004-03-24	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 200–397（198 aa） Fragment：Mature protease domain (residues 200-397)	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；1.3M lithium sulfate, 0.02M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 0.83 Å R-free 0.099
1TAL ALPHA-LYTIC PROTEASE AT 120 K (SINGLE STRUCTURE MODEL) Deposited 1996-10-30	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 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 1.50 Å R-free 0.192
2ALP REFINED STRUCTURE OF ALPHA-LYTIC PROTEASE AT 1.7 ANGSTROMS RESOLUTION. ANALYSIS OF HYDROGEN BONDING AND SOLVENT STRUCTURE Deposited 1985-03-07	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 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
2H5C 0.82A resolution crystal structure of alpha-lytic protease at pH 5 Deposited 2006-05-25	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 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN (RESIDUES 200-397)	Not recorded	SO4 SULFATE ION × 11 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.25；298 K；1.3M LITHIUM SULFATE, 0.02M TRIS, PH 4.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K	Resolution 0.82 Å R-free 0.093
2H5D 0.9A resolution crystal structure of alpha-lytic protease complexed with a transition state analogue, MeOSuc-Ala-Ala-Pro-Val boronic acid Deposited 2006-05-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN (RESIDUES 200-397)	Not recorded	SO4 SULFATE ION × 8 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；298 K；1.3M LITHIUM SULFATE, 0.02M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.00	Resolution 0.90 Å R-free 0.091
2LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
2PRO PRO REGION OF ALPHA-LYTIC PROTEASE Deposited 1998-08-20	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 34–199（166 aa） Fragment：PRO REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.342
2PRO PRO REGION OF ALPHA-LYTIC PROTEASE Deposited 1998-08-20	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 B 34–199（166 aa） Fragment：PRO REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.342
2PRO PRO REGION OF ALPHA-LYTIC PROTEASE Deposited 1998-08-20	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 C 34–199（166 aa） Fragment：PRO REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.342
2PRO PRO REGION OF ALPHA-LYTIC PROTEASE Deposited 1998-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–199（166 aa） Fragment：PRO REGION Chain B 34–199（166 aa） Fragment：PRO REGION Chain C 34–199（166 aa） Fragment：PRO REGION	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.00 Å R-free 0.342
2ULL MULTIPLE CONFORMATION STRUCTURE OF ALPHA-LYTIC PROTEASE AT 120 K Deposited 1996-11-26	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 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 1.50 Å R-free 0.192
3LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
3M7T Crystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant Deposited 2010-03-17	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 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN (RESIDUES 1-198)	Mutation：E8A, R105S	GOL GLYCEROL × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.3 M lithium sulfate, 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.202
3M7U Crystal Structure of Alpha-Lytic Protease SB1+2 R64A/E182Q Mutant Deposited 2010-03-17	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 200–397（198 aa） Fragment：MATURE PROTEASE DOMAIN (RESIDUES 1-198)	Mutation：R64A, E182Q	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.3 M lithium sulfate, 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.05 Å R-free 0.164
3PRO ALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION Deposited 1998-08-26	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 200–397（198 aa） Fragment：MATURE PROTEASE Chain C 34–199（166 aa） Fragment：PRO REGION	Mutation：M158A	AES 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 1.80 Å R-free 0.230
3PRO ALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION Deposited 1998-08-26	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 B 200–397（198 aa） Fragment：MATURE PROTEASE Chain D 34–199（166 aa） Fragment：PRO REGION	Mutation：M158A	AES 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 1.80 Å R-free 0.230
3URC T181G mutant of alpha-Lytic Protease Deposited 2011-11-22	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 200–397（198 aa）	Mutation：T181G	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.3 M lithium sulfate and 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.10 Å R-free 0.136
3URD T181A mutant of alpha-Lytic Protease Deposited 2011-11-22	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 200–397（198 aa） Fragment：UNP residues 200-397	Mutation：T132A	SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.3 M lithium sulfate and 20 mM Tris sulfate, pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.08 Å R-free 0.142
3URE Repack mutant (T181I, W199L, Q210I) of alpha-Lytic Protease Deposited 2011-11-22	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 200–397（198 aa）	Mutation：T181I, W199L, Q210I	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.3 M lithium sulfate, 10 mM CuCl2, and 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.49 Å R-free 0.170
3URE Repack mutant (T181I, W199L, Q210I) of alpha-Lytic Protease Deposited 2011-11-22	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 200–397（198 aa）	Mutation：T181I, W199L, Q210I	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.3 M lithium sulfate, 10 mM CuCl2, and 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.49 Å R-free 0.170
4PRO ALPHA-LYTIC PROTEASE COMPLEXED WITH PRO REGION Deposited 1998-10-01	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 200–397（198 aa） Fragment：CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION Chain C 34–199（166 aa） Fragment：CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION	Mutation：CHAIN A, B, M158A Mutation：CHAIN A, B, M158A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.40 Å R-free 0.238
4PRO ALPHA-LYTIC PROTEASE COMPLEXED WITH PRO REGION Deposited 1998-10-01	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 B 200–397（198 aa） Fragment：CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION Chain D 34–199（166 aa） Fragment：CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION	Mutation：CHAIN A, B, M158A Mutation：CHAIN A, B, M158A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.40 Å R-free 0.238
5LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.13 Å
5WOT NMR solution structure of a-lytic protease using two 4D-spectra Deposited 2017-08-03	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 200–397（198 aa） Fragment：residues 200-397	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 2.0 mM [U-13C; U-15N] alpha-lytic protease protein, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
6LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
7LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.05 Å
8LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
9LPR STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS Deposited 1991-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 200–397（198 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å

48 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRLA_LYSEN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–198； UniProt 200–397 Author chain C； PDBConstruct 1–198； UniProt 200–397

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	3qgj
Deposition date deposition_date	2011-01-24
Structure title title	1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal
Keywords keywords	;serine protease, hydrolase domain, alpha/beta hydrolase, serine proteinase, Hydrolysis, Extracellular, peptide inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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	26.09 Å
Radius of gyration Rg (electron density) rg_electron	25.27 Å
Forward intensity I(0) i0	35028800.00
Molecular weight molecular_weight	41739.0 kDa
Excluded volume excluded_volume	50590 Å³
Envelope volume envelope_volume	60714 Å³
Hydration-shell volume shell_volume	20926 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	31.17 Å
Envelope Rg envelope_rg	25.11 Å
Shape Rg shape_rg	25.23 Å
Total Rg total_rg	26.01 Å
Total atoms total_atoms	2938
Residues n_residues	402
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	82.2 Å
Rg (real space) rg_real	26.23 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.5030e+07
I(0) uncertainty (real space) i0_real_error	5.5600e+05
Rg (reciprocal space) rg_reciprocal	26.19 Å
I(0) (reciprocal space) i0_reciprocal	35030000.0000
Solution quality estimate total_estimate	0.8568
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.737
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8779000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Alpha-lytic protease
Molecular weight formula_weight	19875.1 kDa
EC 编号 ec_number	3.4.21.12
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3757

ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG

Entity 2 Entity 2 polymer

Description description	Ac-AlaAlaPro-Alanal peptide
Molecular weight formula_weight	340.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

XAAPX

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	trifluoroacetic acid
Molecular weight formula_weight	114.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	525

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3qgja_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.1 — Prokaryotic proteases

Domain ID domain_id	d3qgjc_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.1 — Prokaryotic proteases

CATH v4.4 (4 domains)

Domain ID domain_id	3qgjA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3qgjA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3qgjC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3qgjC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	63.936 Å
Unit-cell length b length_b	63.936 Å
Unit-cell length c length_c	316.897 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	26.100 Å
R factor r_factor	0.1680
R_work r_work	0.1670
R_free r_free	0.1920

fit	/app/data/saxs_computation/qg/3qgj/3qgj.fit
pddf	/app/data/pr_computation/qg/3qgj/3qgj.pr.out
profile	/app/data/saxs_computation/qg/3qgj/3qgj.dat

1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal

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

Alpha-lytic protease

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)