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1evi

THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE

Method: X-RAY DIFFRACTION Dmax: 110.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-AMINO ACID OXIDASE

Sus scrofa

UniProt P00371

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 1–340 Chain B； UniProt 1–340 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

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 1EVI 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 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 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 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 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 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 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 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 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 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
1KIF D-AMINO ACID OXIDASE FROM PIG KIDNEY Deposited 1996-01-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–347（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 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 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 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 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
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 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
Chains and sequence ranges Author chain A； PDBConstruct 1–340； UniProt 1–340 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

SAXS profile for 1evi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1evi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1evi
Deposition date deposition_date2000-04-20
Structure title titleTHREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE
Keywords keywordsFLAVOENZYME, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.25 Å
Radius of gyration Rg (electron density) rg_electron29.77 Å
Forward intensity I(0) i096836300.00
Molecular weight molecular_weight78938.0 kDa
Excluded volume excluded_volume98989 ų
Envelope volume envelope_volume113790 ų
Hydration-shell volume shell_volume33634 ų
Envelope diameter envelope_diameter117.6 Å
Shell Rg shell_rg35.17 Å
Envelope Rg envelope_rg30.04 Å
Shape Rg shape_rg29.75 Å
Total Rg total_rg30.31 Å
Total atoms total_atoms5580
Residues n_residues680
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.4 Å
Rg (real space) rg_real30.52 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real9.6840e+07
I(0) uncertainty (real space) i0_real_error1.6440e+06
Rg (reciprocal space) rg_reciprocal30.41 Å
I(0) (reciprocal space) i0_reciprocal96830000.0000
Solution quality estimate total_estimate0.8026
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.7 Å
Skewness Skewness skewness0.619
Kurtosis Kurtosis kurtosis0.010
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42410000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.617; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.900
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1evia1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.4 — Nucleotide-binding domain
Superfamily Superfamily superfamilyc.4.1 — Nucleotide-binding domain
Family Family familyc.4.1.2 — D-aminoacid oxidase, N-terminal domain
Domain ID domain_idd1evia2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.3 — D-aminoacid oxidase-like
Domain ID domain_idd1evib1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.4 — Nucleotide-binding domain
Superfamily Superfamily superfamilyc.4.1 — Nucleotide-binding domain
Family Family familyc.4.1.2 — D-aminoacid oxidase, N-terminal domain
Domain ID domain_idd1evib2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.3 — D-aminoacid oxidase-like

CATH v4.4 (4 domains)

Domain ID domain_id1eviA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1eviA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-Amino Acid Oxidase, subunit A, domain 2
Domain ID domain_id1eviB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1eviB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-Amino Acid Oxidase, subunit A, domain 2
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8. Citations (1)

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9. Files and Curves (10)