1dao

COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID

Method: X-RAY DIFFRACTION D_max: 174.7 Å Quality: GOOD

▼

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

D-AMINO ACID OXIDASE

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–347 Chain E； UniProt 1–347	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–347 Chain F； UniProt 1–347	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–347 Chain G； UniProt 1–347	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
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–347 Chain H； UniProt 1–347	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
5	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–347 Chain D； UniProt 1–347 Chain G； UniProt 1–347 Chain H； UniProt 1–347	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
6	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–347 Chain B； UniProt 1–347 Chain E； UniProt 1–347 Chain F； UniProt 1–347	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

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 1DAO	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 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
1DDO REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP Deposited 1997-01-16	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
4YJG Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane 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 1–340（340 aa） Fragment：UNP residues 1-340	Mutation：Y228L, R283G 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
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 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 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 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 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 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 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 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 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 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OXDA_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–347； UniProt 1–347 Author chain B； PDBConstruct 1–347； UniProt 1–347 Author chain C； PDBConstruct 1–347； UniProt 1–347 Author chain D； PDBConstruct 1–347； UniProt 1–347 Author chain E； PDBConstruct 1–347； UniProt 1–347 Author chain F； PDBConstruct 1–347； UniProt 1–347 Author chain G； PDBConstruct 1–347； UniProt 1–347 Author chain H； PDBConstruct 1–347； UniProt 1–347

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	1dao
Deposition date deposition_date	1997-01-16
Structure title title	COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID
Keywords keywords	FLAVOENZYME, FAD COFACTOR, OXIDOREDUCTASE; FLAVOENZYME
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	50.69 Å
Radius of gyration Rg (electron density) rg_electron	50.45 Å
Forward intensity I(0) i0	1388240000.00
Molecular weight molecular_weight	314370.0 kDa
Excluded volume excluded_volume	394250 Å³
Envelope volume envelope_volume	511710 Å³
Hydration-shell volume shell_volume	84462 Å³
Envelope diameter envelope_diameter	186.3 Å
Shell Rg shell_rg	54.20 Å
Envelope Rg envelope_rg	49.67 Å
Shape Rg shape_rg	50.44 Å
Total Rg total_rg	50.60 Å
Total atoms total_atoms	22224
Residues n_residues	2712
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	174.7 Å
Rg (real space) rg_real	50.79 Å
Rg uncertainty (real space) rg_real_error	1.84 Å
I(0) (real space) i0_real	1.3880e+09
I(0) uncertainty (real space) i0_real_error	2.9120e+07
Rg (reciprocal space) rg_reciprocal	50.59 Å
I(0) (reciprocal space) i0_reciprocal	1388000000.0000
Solution quality estimate total_estimate	0.8591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	56.4 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.281
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	66270000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.756

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	D-AMINO ACID OXIDASE
Molecular weight formula_weight	39377.8 kDa
EC 编号 ec_number	1.4.3.3
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	22232

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLLTMPPSHL

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE
Molecular weight formula_weight	855.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

▼

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1daoa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daoa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daob1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daob2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daoc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daoc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daod1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daod2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daoe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daoe2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daof1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daof2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daog1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daog2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1daoh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.2 — D-aminoacid oxidase, N-terminal domain

Domain ID domain_id	d1daoh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

CATH v4.4 (16 domains)

Domain ID domain_id	1daoA01
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	1daoA02
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	1daoB01
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	1daoB02
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	1daoC01
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	1daoC02
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	1daoD01
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	1daoD02
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	1daoE01
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	1daoE02
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	1daoF01
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	1daoF02
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	1daoG01
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	1daoG02
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	1daoH01
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	1daoH02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	326.400 Å
Unit-cell length b length_b	136.900 Å
Unit-cell length c length_c	196.500 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	64

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2600

fit	/app/data/saxs_computation/da/1dao/1dao.fit
pddf	/app/data/pr_computation/da/1dao/1dao.pr.out
profile	/app/data/saxs_computation/da/1dao/1dao.dat