1ddo

REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP

Method: X-RAY DIFFRACTION D_max: 173.4 Å Quality: GOOD

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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	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
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	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
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	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
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	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
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	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
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	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

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 1DDO	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
1DAO COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID 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	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 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 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 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 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 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
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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ddo
Deposition date deposition_date	1997-01-16
Structure title title	REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP
Keywords keywords	FLAVOENZYME, FAD COFACTOR, OXIDOREDUCTASE; FLAVOENZYME
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	50.59 Å
Radius of gyration Rg (electron density) rg_electron	50.36 Å
Forward intensity I(0) i0	1402100000.00
Molecular weight molecular_weight	315830.0 kDa
Excluded volume excluded_volume	395980 Å³
Envelope volume envelope_volume	513470 Å³
Hydration-shell volume shell_volume	84864 Å³
Envelope diameter envelope_diameter	184.2 Å
Shell Rg shell_rg	54.25 Å
Envelope Rg envelope_rg	49.56 Å
Shape Rg shape_rg	50.35 Å
Total Rg total_rg	50.52 Å
Total atoms total_atoms	22334
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

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

Maximum dimension Dmax dmax	173.4 Å
Rg (real space) rg_real	50.69 Å
Rg uncertainty (real space) rg_real_error	1.69 Å
I(0) (real space) i0_real	1.4020e+09
I(0) uncertainty (real space) i0_real_error	2.7400e+07
Rg (reciprocal space) rg_reciprocal	50.49 Å
I(0) (reciprocal space) i0_reciprocal	1402000000.0000
Solution quality estimate total_estimate	0.8609
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	56.0 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.284
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	65520000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.746

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

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	22441

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLLTMPPSHL

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	IMINO-TRYPTOPHAN
Molecular weight formula_weight	202.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	D-TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1ddoa1
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	d1ddoa2
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	d1ddob1
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	d1ddob2
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	d1ddoc1
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	d1ddoc2
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	d1ddod1
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	d1ddod2
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	d1ddoe1
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	d1ddoe2
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	d1ddof1
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	d1ddof2
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	d1ddog1
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	d1ddog2
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	d1ddoh1
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	d1ddoh2
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	1ddoA01
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	1ddoA02
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	1ddoB01
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	1ddoB02
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	1ddoC01
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	1ddoC02
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	1ddoD01
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	1ddoD02
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	1ddoE01
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	1ddoE02
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	1ddoF01
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	1ddoF02
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	1ddoG01
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	1ddoG02
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	1ddoH01
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	1ddoH02
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	325.200 Å
Unit-cell length b length_b	137.100 Å
Unit-cell length c length_c	196.800 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	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2500

fit	/app/data/saxs_computation/dd/1ddo/1ddo.fit
pddf	/app/data/pr_computation/dd/1ddo/1ddo.pr.out
profile	/app/data/saxs_computation/dd/1ddo/1ddo.dat