2ylj

Horse Radish Peroxidase, mutant S167Y

Method: X-RAY DIFFRACTION D_max: 64.5 Å Quality: GOOD

▼

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

PEROXIDASE C1A

ARMORACIA RUSTICANA

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 31–336	Fragment：RESIDUES 31-336 Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7	Resolution 1.69 Å R-free 0.189

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 2YLJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ATJ RECOMBINANT HORSERADISH PEROXIDASE C1A Deposited 1997-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 31–336（306 aa） Chain B 31–336（306 aa） Chain C 31–336（306 aa） Chain D 31–336（306 aa） Chain E 31–336（306 aa） Chain F 31–336（306 aa）	Not recorded	CA CALCIUM ION × 12 HEM PROTOPORPHYRIN IX CONTAINING FE × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% (W/V) PEG 4000, 0.2 M ZINC ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 2.15 Å R-free 0.242
1GW2 RECOMBINANT HORSERADISH PEROXIDASE C1A THR171SER IN COMPLEX WITH FERULIC ACID Deposited 2002-03-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% PEG 4000, 0.2 M CALCIUM ACETATE,0.1 M CACODYLATE BUFFER PH 6.5	Resolution 2.15 Å R-free 0.211
1GWO Recombinant horseradish peroxidase C1A ALA170GLN Deposited 2002-03-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER PH 6.5	Resolution 2.07 Å R-free 0.221
1GWT RECOMBINANT HORSERADISH PEROXIDASE C1A PHE221MET Deposited 2002-03-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 NA SODIUM ION × 1 FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.70 Å R-free 0.198
1GWU RECOMBINANT HORSERADISH PEROXIDASE C1A ALA140GLY Deposited 2002-03-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Mutation：YES	NA SODIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16%(W/V)PEG4000,0.2M CALCIUM ACETATE,0.1M CACODYLATE PH6.5, pH 6.50	Resolution 1.31 Å R-free 0.193
1GX2 Recombinant horseradish peroxidase Phe209Ser complex with benzhydroxamic acid Deposited 2002-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.197
1GX2 Recombinant horseradish peroxidase Phe209Ser complex with benzhydroxamic acid Deposited 2002-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–338（308 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.20 Å R-free 0.197
1H55 STRUCTURE OF HORSERADISH PEROXIDASE C1A COMPOUND II Deposited 2001-05-18	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 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 O OXYGEN ATOM × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.61 Å R-free 0.210
1H57 Structure of horseradish peroxidase C1A compound III Deposited 2001-05-20	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 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 OXY OXYGEN MOLECULE × 1 PEO HYDROGEN PEROXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.196
1H58 STRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A Deposited 2001-05-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5 THE FERROUS STATE WAS FORMED BY SOAKING THE CRYSTALS FOR 30 MINUTES IN A RESERVOIR SOLUTION SUPPLEMENTED WITH 100 MM SODIUM DITHIONITE AND PEG400 BEFORE FLASH FREEZING	Resolution 1.70 Å R-free 0.200
1H5A STRUCTURE OF FERRIC HORSERADISH PEROXIDASE C1A IN COMPLEX WITH ACETATE Deposited 2001-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.202
1H5C X-ray induced reduction of horseradish peroxidase C1A Compound III (100-200% dose) Deposited 2001-05-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.62 Å R-free 0.198
1H5D X-ray induced reduction of horseradish peroxidase C1A Compound III (0-11% dose) Deposited 2001-05-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.220
1H5E X-ray induced reduction of horseradish peroxidase C1A Compound III (11-22% dose) Deposited 2001-05-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.223
1H5F X-ray induced reduction of horseradish peroxidase C1A Compound III (22-33% dose) Deposited 2001-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.220
1H5G X-ray induced reduction of horseradish peroxidase C1A Compound III (33-44% dose) Deposited 2001-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.223
1H5H X-ray induced reduction of horseradish peroxidase C1A Compound III (44-56% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 11	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.218
1H5I X-ray induced reduction of horseradish peroxidase C1A Compound III (56-67% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.216
1H5J X-ray induced reduction of horseradish peroxidase C1A Compound III (67-78% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.221
1H5K X-ray induced reduction of horseradish peroxidase C1A Compound III (78-89% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.213
1H5L X-ray induced reduction of horseradish peroxidase C1A Compound III (89-100% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.219
1H5M X-ray induced reduction of horseradish peroxidase C1A Compound III (0-100% dose) Deposited 2001-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 PEO HYDROGEN PEROXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.60 Å R-free 0.198
1HCH Structure of horseradish peroxidase C1A compound I Deposited 2001-05-04	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 31–336（306 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 1 CA CALCIUM ION × 2 O OXYGEN ATOM × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.57 Å R-free 0.203
1KZM Distal Heme Pocket Mutant (R38S/H42E) of Recombinant Horseradish Peroxidase C (HRP C). Deposited 2002-02-07	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 31–338（308 aa） Fragment：Horseradish Peroxidase C1A (HRP C)	Mutation：R38S/H42E	CA CALCIUM ION × 2 CAC CACODYLATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；PEG-8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.00 Å R-free 0.203
1W4W Ferric horseradish peroxidase C1A in complex with formate Deposited 2004-08-03	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 31–353（323 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；20% PEG8000, 0.2M CA-ACETATE, 0.1 M NA-CACODYLATE PH 6.5, FERULIC ACID AS ADDITIVE STREAK SEEDING, HANGING DROP, 4DEGC	Resolution 1.55 Å R-free 0.215
1W4Y Ferrous horseradish peroxidase C1A in complex with carbon monoxide Deposited 2004-08-03	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 31–353（323 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 CMO CARBON MONOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；20% PEG8000, 0.2 M CA-ACETATE, 0.1 M NA-CACODYLATE PH 6.5, FERULIC ACID AS ADDITIVE, HANGING DROP, STREAK SEEDING, 4DEGC	Resolution 1.60 Å R-free 0.211
2ATJ RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID Deposited 1997-08-19	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 31–337（307 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.00 Å R-free 0.198
2ATJ RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID Deposited 1997-08-19	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 B 31–337（307 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.00 Å R-free 0.198
3ATJ HEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID Deposited 1998-12-16	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 31–338（308 aa） Chain B 31–338（308 aa）	Mutation：F221M Mutation：F221M	CA CALCIUM ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 BHO BENZHYDROXAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.203
4ATJ DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID Deposited 1999-04-19	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 30–338（309 aa）	Mutation：H42E	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.194
4ATJ DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID Deposited 1999-04-19	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 B 30–338（309 aa）	Mutation：H42E	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.50 Å R-free 0.194
6ATJ RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID Deposited 1999-04-23	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 31–338（308 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 2.00 Å R-free 0.199
7ATJ RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID Deposited 1999-04-26	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 31–338（308 aa）	Not recorded	CA CALCIUM ION × 2 CYN CYANIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5	Resolution 1.47 Å R-free 0.203
9H1M Recombinant ferric horseradish peroxidase C1A Deposited 2024-10-09	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 31–338（308 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 5 2HP DIHYDROGENPHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；25% (w/v) PEG 1500, 100 mM SPG (2:7:7, succinic acid:sodium hydrogen phosphate:glycine buffer pH 8.5	Resolution 1.63 Å R-free 0.189

31 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PER1A_ARMRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 31–336

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ylj
Deposition date deposition_date	2011-06-02
Structure title title	Horse Radish Peroxidase, mutant S167Y
Keywords keywords	OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.02 Å
Radius of gyration Rg (electron density) rg_electron	18.97 Å
Forward intensity I(0) i0	21004100.00
Molecular weight molecular_weight	34398.0 kDa
Excluded volume excluded_volume	42781 Å³
Envelope volume envelope_volume	47033 Å³
Hydration-shell volume shell_volume	20571 Å³
Envelope diameter envelope_diameter	66.3 Å
Shell Rg shell_rg	25.51 Å
Envelope Rg envelope_rg	19.31 Å
Shape Rg shape_rg	18.95 Å
Total Rg total_rg	19.89 Å
Total atoms total_atoms	2418
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

▼

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

Maximum dimension Dmax dmax	64.5 Å
Rg (real space) rg_real	19.95 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.1000e+07
I(0) uncertainty (real space) i0_real_error	2.3760e+05
Rg (reciprocal space) rg_reciprocal	19.97 Å
I(0) (reciprocal space) i0_reciprocal	21000000.0000
Solution quality estimate total_estimate	0.8926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.7 Å
Skewness Skewness skewness	0.272
Kurtosis Kurtosis kurtosis	-0.305
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4884000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PEROXIDASE C1A
Molecular weight formula_weight	33823.1 kDa
EC 编号 ec_number	1.11.1.7
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2937

QLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALYGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNS

来源 Source

来源生物 organism	ARMORACIA RUSTICANA
通用名 common_name	HORSERADISH
NCBI Class编号 ncbi_taxonomy_id	3704
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	431

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ylja_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

CATH v4.4 (2 domains)

Domain ID domain_id	2yljA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2yljA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

▶

8. Citations (1)

▶

Unit-cell length a length_a	40.400 Å
Unit-cell length b length_b	67.370 Å
Unit-cell length c length_c	117.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	44.336 Å
R factor r_factor	0.1542
R_work r_work	0.1524
R_free r_free	0.1888

fit	/app/data/saxs_computation/yl/2ylj/2ylj.fit
pddf	/app/data/pr_computation/yl/2ylj/2ylj.pr.out
profile	/app/data/saxs_computation/yl/2ylj/2ylj.dat