1u67

Crystal Structure of Arachidonic Acid Bound to a Mutant of Prostagladin H Synthase-1 that Forms Predominantly 11-HPETE.

Method: X-RAY DIFFRACTION Dmax: 78.4 Å Quality: EXCELLENT

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

Prostaglandin G/H synthase 1 precursor

Ovis aries

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 A; UniProt 1–600 Mutation:V349A,W387F 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;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 BOG octyl beta-D-glucopyranoside × 8 COH PROTOPORPHYRIN IX CONTAINING CO × 2 ACD ARACHIDONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;273 K;Sodium Citrate, Lithium Chloride, Sodium Azide, N-Octyl Glucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K Resolution 3.10 Å R-free 0.311

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 A; 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 1u67

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1u67
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1u67
Deposition date deposition_date2004-07-29
Structure title titleCrystal Structure of Arachidonic Acid Bound to a Mutant of Prostagladin H Synthase-1 that Forms Predominantly 11-HPETE.
Keywords keywordscyclooxgenase, arachidonic acid, heme, eicosanoid, 11-HETE, COX-1, COX-2, 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_electron23.97
Forward intensity I(0) i063905300.00
Molecular weight molecular_weight64460.0 kDa
Excluded volume excluded_volume81317 ų
Envelope volume envelope_volume95537 ų
Hydration-shell volume shell_volume32104 ų
Envelope diameter envelope_diameter79.4
Shell Rg shell_rg32.17
Envelope Rg envelope_rg24.34
Shape Rg shape_rg23.95
Total Rg total_rg24.95
Total atoms total_atoms4551
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 dmax78.4
Rg (real space) rg_real24.97
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real6.3910e+07
I(0) uncertainty (real space) i0_real_error7.2730e+05
Rg (reciprocal space) rg_reciprocal25.01
I(0) (reciprocal space) i0_reciprocal63910000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9701000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.988

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1u67a1
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_idd1u67a2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module

CATH v4.4 (2 domains)

Domain ID domain_id1u67A01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id1u67A02
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)