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1c0k

CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE

Method: X-RAY DIFFRACTION Dmax: 74.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (D-AMINO ACID OXIDASE)

Rhodosporidium toruloides

UniProt P80324

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 1–361 Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 LAC LACTIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50 Resolution 1.46 Å

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 1C0K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C0I CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES Deposited 1999-07-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–361（361 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 BE2 2-AMINOBENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100MM HEPES, POLYETHYLENE GLYCOL 10000, 200MM AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.249
1C0L D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION Deposited 1999-07-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–361（361 aa）
Not recorded FLA TRIFLUOROALANINE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；100MM HEPES 16% POLYETHYLENE GLYCOL PEG 200MM AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.73 Å R-free 0.204
1C0P D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES Deposited 1999-07-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–361（361 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DAL D-ALANINE × 2 PER PEROXIDE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 MM HEPES 200 MM AMMONIUM SULFATE 16% POLYETHYLENE GLYCOL (PEG) 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.150

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OXDA_RHOTO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–363； UniProt 1–361

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 1c0k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c0k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c0k
Deposition date deposition_date1999-07-16
Structure title titleCRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE
Keywords keywordsFLAVIN CONTAINING PROTEIN, ALPHA-BETA-ALPHA MOTIF, 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_guinier22.17 Å
Radius of gyration Rg (electron density) rg_electron21.31 Å
Forward intensity I(0) i029120900.00
Molecular weight molecular_weight40443.0 kDa
Excluded volume excluded_volume50256 ų
Envelope volume envelope_volume58275 ų
Hydration-shell volume shell_volume22921 ų
Envelope diameter envelope_diameter80.4 Å
Shell Rg shell_rg28.16 Å
Envelope Rg envelope_rg22.16 Å
Shape Rg shape_rg21.27 Å
Total Rg total_rg22.29 Å
Total atoms total_atoms2847
Residues n_residues363
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 dmax74.6 Å
Rg (real space) rg_real22.22 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real2.9120e+07
I(0) uncertainty (real space) i0_real_error3.7280e+05
Rg (reciprocal space) rg_reciprocal22.21 Å
I(0) (reciprocal space) i0_reciprocal29120000.0000
Solution quality estimate total_estimate0.7851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.485
Kurtosis Kurtosis kurtosis-0.071
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9268000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.000
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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) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1c0ka1
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_idd1c0ka2
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_idd1c0ka3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id1c0kA01
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_id1c0kA02
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)