4yjg

Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)

Method: X-RAY DIFFRACTION D_max: 112.8 Å Quality: GOOD

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

D-amino-acid oxidase

Sus scrofa

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–341 Chain B； UniProt 1–340	Fragment：UNP residues 1-341 Mutation：Y228L, R283G Fragment：UNP residues 1-340 Mutation：Y288L, R283G	4DD (2R)-4-phenylbutan-2-amine × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris-HCl (8.5), 0.2M Lithium sulfate	Resolution 2.50 Å R-free 0.237

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 4YJG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AN9 D-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE Deposited 1997-06-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–340（340 aa） Chain B 1–340（340 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BE2 2-AMINOBENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED FROM 120MM SODIUM ACETATE, 60MM SODIUM CITRATE, 30% PEG4000, pH 6.3	Resolution 2.50 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain E 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–347（347 aa） Chain G 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–347（347 aa） Chain D 1–347（347 aa） Chain G 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID Deposited 1997-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–347（347 aa） Chain B 1–347（347 aa） Chain E 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAB FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID	Resolution 3.20 Å R-free 0.260
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain E 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ITR IMINO-TRYPTOPHAN × 2 DTR D-TRYPTOPHAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ITR IMINO-TRYPTOPHAN × 2 DTR D-TRYPTOPHAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–347（347 aa） Chain G 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ITR IMINO-TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ITR IMINO-TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–347（347 aa） Chain D 1–347（347 aa） Chain G 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 ITR IMINO-TRYPTOPHAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–347（347 aa） Chain B 1–347（347 aa） Chain E 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 ITR IMINO-TRYPTOPHAN × 4 DTR D-TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP	Resolution 3.10 Å R-free 0.250
1EVI THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE Deposited 2000-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–340（340 aa） Chain B 1–340（340 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 2PC 3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；PEG 4000, sodium acetate, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.298
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain E 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BEZ BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BEZ BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–347（347 aa） Chain G 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BEZ BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BEZ BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–347（347 aa） Chain D 1–347（347 aa） Chain G 1–347（347 aa） Chain H 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 BEZ BENZOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–347（347 aa） Chain B 1–347（347 aa） Chain E 1–347（347 aa） Chain F 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 BEZ BENZOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；293K	Resolution 2.60 Å
1VE9 Porcine kidney D-amino acid oxidase Deposited 2004-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain B 1–347（347 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BEZ BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；PEG4000, Tris-acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.254
3WGT Crystal structure of D-amino acid oxidase mutant Deposited 2013-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain B 1–347（347 aa）	Mutation：Y228L,R283G Mutation：Y228L,R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 QSC (1R)-1-phenylethanamine × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% Polyethylene glycole 4000, 0.1M TRIS hydrochloride, 0.2M Lithium sulfate monohydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.88 Å R-free 0.230
4YJD Crystal structure of DAAO(Y228L/R283G) variant (apo form) Deposited 2015-03-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–340（340 aa） Fragment：UNP residues 1-340 Chain B 1–340（340 aa） Fragment：UNP residues 1-340	Mutation：Y228L, R283G Mutation：Y228L, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris-HCl(8.5), 0.2M Lithium sulfate	Resolution 2.30 Å R-free 0.250
4YJF Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form) Deposited 2015-03-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–341（341 aa） Fragment：UNP residues 1-341 Chain B 1–339（339 aa） Fragment：UNP residues 1-339	Mutation：Y228L, R283G Mutation：Y228L, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 4 98B (1S)-1-phenylethanamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1M Tris-HCl(pH 8.5), 0.2M Lithium sulfate	Resolution 2.20 Å R-free 0.226
4YJH Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form) Deposited 2015-03-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–340（340 aa） Fragment：UNP residues 1-340 Chain B 1–340（340 aa） Fragment：UNP residues 1-340	Mutation：Y228L, R283G Mutation：Y228L, R283G	96B (2R)-2-phenylpyrrolidine × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.1MTris-HCl(8.5), 0.2M Lithium sulfate	Resolution 2.70 Å R-free 0.263
5WWV Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain B 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 7V3 (S)-(4-chlorophenyl)-phenyl-methanamine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.20 Å R-free 0.242
5WWV Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–347（347 aa） Chain D 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 7V3 (S)-(4-chlorophenyl)-phenyl-methanamine × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.20 Å R-free 0.242
5WWV Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–347（347 aa） Chain F 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 7V3 (S)-(4-chlorophenyl)-phenyl-methanamine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 7 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.20 Å R-free 0.242
5WWV Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–347（347 aa） Chain H 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 7V3 (S)-(4-chlorophenyl)-phenyl-methanamine × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.20 Å R-free 0.242
5WX2 Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–347（347 aa） Chain B 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 8 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.00 Å R-free 0.253
5WX2 Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–347（347 aa） Chain D 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.00 Å R-free 0.253
5WX2 Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–347（347 aa） Chain F 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.00 Å R-free 0.253
5WX2 Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) Deposited 2017-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–347（347 aa） Chain H 1–347（347 aa）	Mutation：I230A, R283G Mutation：I230A, R283G	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5	Resolution 3.00 Å R-free 0.253

12 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OXDA_PIG
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–341； UniProt 1–341 Author chain B； PDBConstruct 1–340； UniProt 1–340

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	4yjg
Deposition date deposition_date	2015-03-03
Structure title title	Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)
Keywords keywords	amine oxidase, Variant of D-amino acid oxidase, S-methylbenzylamine binding form, OXIDOREDUCTASE; OXIDOREDUCTASE
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	30.51 Å
Radius of gyration Rg (electron density) rg_electron	29.95 Å
Forward intensity I(0) i0	97568200.00
Molecular weight molecular_weight	78987.0 kDa
Excluded volume excluded_volume	98972 Å³
Envelope volume envelope_volume	118550 Å³
Hydration-shell volume shell_volume	34529 Å³
Envelope diameter envelope_diameter	119.2 Å
Shell Rg shell_rg	35.58 Å
Envelope Rg envelope_rg	30.41 Å
Shape Rg shape_rg	29.93 Å
Total Rg total_rg	30.51 Å
Total atoms total_atoms	5577
Residues n_residues	681
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	112.8 Å
Rg (real space) rg_real	30.78 Å
Rg uncertainty (real space) rg_real_error	1.49 Å
I(0) (real space) i0_real	9.7570e+07
I(0) uncertainty (real space) i0_real_error	1.6110e+06
Rg (reciprocal space) rg_reciprocal	30.67 Å
I(0) (reciprocal space) i0_reciprocal	97560000.0000
Solution quality estimate total_estimate	0.7954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.620
Kurtosis Kurtosis kurtosis	0.020
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	43850000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.570; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.677; Smooth: 0.978

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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	D-amino-acid oxidase
Molecular weight formula_weight	38563.8 kDa
EC 编号 ec_number	1.4.3.3
Mutation mutation	Y228L, R283G
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	5629

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPLIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFGPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLLT

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	Pig
NCBI Class编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	D-amino-acid oxidase
Molecular weight formula_weight	38462.7 kDa
EC 编号 ec_number	1.4.3.3
Mutation mutation	Y288L, R283G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	Pig
NCBI Class编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	(2R)-4-phenylbutan-2-amine
Molecular weight formula_weight	149.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	52

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4yjgA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	4yjgA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

Domain ID domain_id	4yjgB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	4yjgB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	68.590 Å
Unit-cell length b length_b	92.114 Å
Unit-cell length c length_c	110.274 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	2.500 Å
Low-resolution limit resolution_low	23.000 Å
R factor r_factor	0.1921
R_work r_work	0.1898
R_free r_free	0.2366

fit	/app/data/saxs_computation/yj/4yjg/4yjg.fit
pddf	/app/data/pr_computation/yj/4yjg/4yjg.pr.out
profile	/app/data/saxs_computation/yj/4yjg/4yjg.dat

Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)

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

D-amino-acid oxidase

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

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) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)