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1dao

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

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-AMINO ACID OXIDASE

OrganismNot specified

UniProt P00371

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2 water × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2 water × 2 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 2 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 2 water × 2 Consistent with protein count
5 Protein homooligomer Homooligomer Protein 4 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 4 water × 4 Consistent with protein count
6 Protein homooligomer Homooligomer Protein 4 FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1an9 1dao 1dao 1dao 1dao 1ddo 1ddo 1ddo 1ddo 1evi 1kif 1kif

28 assemblies; showing the first 12

Homotetramer
1dao 1dao 1ddo 1ddo 1kif 1kif

6 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dao
Deposition date deposition_date1997-01-16
Structure title titleCOVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID
Keywords keywordsFLAVOENZYME, FAD COFACTOR, OXIDOREDUCTASE; FLAVOENZYME
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1dao__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1dao__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1dao__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）30.38 Å
Rg (electron density)29.85 Å
Total Rg30.40 Å
Atom count5556
Residues678
Excluded volume98562 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1dao__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1dao__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1dao__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1dao__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1dao__assembly_5__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1dao__assembly_6__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1daoa1
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_idd1daoa2
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_idd1daob1
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_idd1daob2
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_idd1daoc1
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_idd1daoc2
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_idd1daod1
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_idd1daod2
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_idd1daoe1
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_idd1daoe2
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_idd1daof1
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_idd1daof2
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_idd1daog1
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_idd1daog2
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_idd1daoh1
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_idd1daoh2
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 (16 domains)

Domain ID domain_id1daoA01
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_id1daoA02
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_id1daoB01
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_id1daoB02
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_id1daoC01
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_id1daoC02
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_id1daoD01
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_id1daoD02
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_id1daoE01
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_id1daoE02
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_id1daoF01
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_id1daoF02
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_id1daoG01
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_id1daoG02
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_id1daoH01
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_id1daoH02
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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7. Citations (1)