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2vd0

Complex structure of prostaglandin D2 synthase at 2.2A.

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

GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE

HOMO SAPIENS

UniProt O60760

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 GLUTATHIONE × 2 2-{[(2E)-3-(3,4-dimethoxyphenyl)prop-2-enoyl]amino}benzoic acid × 1 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 GLUTATHIONE × 1 GLYCEROL × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1iyh 1iyh 1iyi 1iyi 1v40 1v40 2cvd 2cvd 2vcq 2vcq 2vcw 2vcw

49 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name PTGD2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–199； UniProt 1–199 Author chain B； PDBConstruct 1–199； UniProt 1–199 Author chain C； PDBConstruct 1–199； UniProt 1–199 Author chain D； PDBConstruct 1–199； UniProt 1–199

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_id2vd0
Deposition date deposition_date2007-09-28
Structure title titleComplex structure of prostaglandin D2 synthase at 2.2A.
Keywords keywordsPROSTAGLANDIN BIOSYNTHESIS, FATTY ACID BIOSYNTHESIS, PROSTAGLANDIN D2 SYNTHASE, PGDS, ASTHMA, CYTOPLASM, ISOMERASE, LIPID SYNTHESIS; ISOMERASE
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.

2vd0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2vd0__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2vd0__assembly_2__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）22.11 Å
Rg (electron density)20.80 Å
Total Rg21.71 Å
Atom count3302
Residues396
Excluded volume59094 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2vd0__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2vd0__assembly_2__model_1 dimeric （2） 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 (5)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2vd0a1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd2vd0a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches
Domain ID domain_idd2vd0b1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd2vd0b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches
Domain ID domain_idd2vd0c1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd2vd0c2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches
Domain ID domain_idd2vd0d1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd2vd0d2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id2vd0A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2vd0A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2vd0B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2vd0B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2vd0C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2vd0C02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2vd0D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2vd0D02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10 —
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7. Citations (1)