1cvu

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2

Method: X-RAY DIFFRACTION Dmax: 99.1 Å Quality: EXCELLENT

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

PROSTAGLANDIN H2 SYNTHASE-2

Mus musculus

UniProt Q05769

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 Heteromer Protein × 3 其他Polymer 4 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 18–569 Chain B; UniProt 18–569 Fragment:PROSTAGLANDIN H2 SYNTHASE-2 Mutation:H207A (COX-1 NUMBERING) PROTEIN (9-MER) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BOG octyl beta-D-glucopyranoside × 5 ACD ARACHIDONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;291 K;MONOMETHYL PEG 550, MAGNESIUM SULFATE, ARACHIDNOIC ACID, EPPS, B-OG, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.235

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.

47 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PGH2_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–552; UniProt 18–569 Author chain B; PDBConstruct 1–552; UniProt 18–569

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 1cvu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cvu
Deposition date deposition_date1999-08-24
Structure title titleCRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2
Keywords keywordsCOX-2, CYCLOOXYGENASE, PROSTAGLANDIN, ARACHIDONATE, ENDOPEROXIDE, OXIDOREDUCTASE-peptide complex; OXIDOREDUCTASE/peptide
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.25
Radius of gyration Rg (electron density) rg_electron31.35
Forward intensity I(0) i0254606000.00
Molecular weight molecular_weight132360.0 kDa
Excluded volume excluded_volume167300 ų
Envelope volume envelope_volume198590 ų
Hydration-shell volume shell_volume50566 ų
Envelope diameter envelope_diameter102.9
Shell Rg shell_rg40.19
Envelope Rg envelope_rg31.28
Shape Rg shape_rg31.32
Total Rg total_rg32.17
Total atoms total_atoms9329
Residues n_residues1113
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 dmax99.1
Rg (real space) rg_real32.09
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real2.5460e+08
I(0) uncertainty (real space) i0_real_error3.5900e+06
Rg (reciprocal space) rg_reciprocal32.16
I(0) (reciprocal space) i0_reciprocal254600000.0000
Solution quality estimate total_estimate0.9011
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.4
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61650000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.898

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1cvua1
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_idd1cvua2
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
Domain ID domain_idd1cvub1
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_idd1cvub2
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 (4 domains)

Domain ID domain_id1cvuA01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id1cvuA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology640 — Myeloperoxidase, subunit C
Homologous superfamily homologous superfamily10 — Haem peroxidase domain superfamily, animal type
Domain ID domain_id1cvuB01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id1cvuB02
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 (2)

9. Files and Curves (10)