2oye

Indomethacin-(R)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1

Method: X-RAY DIFFRACTION Dmax: 77.8 Å Quality: REASONABLE

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

Prostaglandin G/H synthase 1

OrganismNot specified

UniProt P05979

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 6 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 1–600 Not recorded 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BOG octyl beta-D-glucopyranoside × 4 FLC CITRATE ANION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 IM8 2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1R)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;273 K;Sodium Citrate, Lithium Chloride, Sodium Azide, and beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K Resolution 2.85 Å R-free 0.292

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.

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PGH1_SHEEP
Isoform
PDB entities 1
Chains and sequence ranges Author chain P; PDBConstruct 1–600; UniProt 1–600

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 2oye

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2oye
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2oye
Deposition date deposition_date2007-02-21
Structure title titleIndomethacin-(R)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1
Keywords keywordsCOX, PGHS, indomethacin, NSAID, heme, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.09
Radius of gyration Rg (electron density) rg_electron23.96
Forward intensity I(0) i064769800.00
Molecular weight molecular_weight64880.0 kDa
Excluded volume excluded_volume81804 ų
Envelope volume envelope_volume95133 ų
Hydration-shell volume shell_volume32063 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg32.15
Envelope Rg envelope_rg24.27
Shape Rg shape_rg23.94
Total Rg total_rg24.92
Total atoms total_atoms4578
Residues n_residues553
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax77.8
Rg (real space) rg_real24.97
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real6.4770e+07
I(0) uncertainty (real space) i0_real_error8.4930e+05
Rg (reciprocal space) rg_reciprocal25.01
I(0) (reciprocal space) i0_reciprocal64770000.0000
Solution quality estimate total_estimate0.7261
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.9
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.388
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10180000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.994; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2oyep1
Class classa — All alpha proteins
Fold Fold folda.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamilya.93.1 — Heme-dependent peroxidases
Family Family familya.93.1.2 — Myeloperoxidase-like
Domain ID domain_idd2oyep2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2oyeP01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id2oyeP02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology640 — Myeloperoxidase, subunit C
Homologous superfamily homologous superfamily10 — Haem peroxidase domain superfamily, animal type

8. Citations (1)

9. Files and Curves (10)