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2cvd

Crystal structure analysis of human hematopoietic prostaglandin D synthase complexed with HQL-79

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 MAGNESIUM ION × 1 GLUTATHIONE × 2 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE × 2 GLYCEROL × 1 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 MAGNESIUM ION × 1 GLUTATHIONE × 2 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE × 2 GLYCEROL × 6 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 1–198； UniProt 1–198 Author chain B； PDBConstruct 1–198； UniProt 1–198 Author chain C； PDBConstruct 1–198； UniProt 1–198 Author chain D； PDBConstruct 1–198； UniProt 1–198

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_id2cvd
Deposition date deposition_date2005-06-02
Structure title titleCrystal structure analysis of human hematopoietic prostaglandin D synthase complexed with HQL-79
Keywords keywordsglutathione-S-transferase, Isomerase; 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.

2cvd__assembly_2__model_1

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

Download this curve (.dat)

2cvd__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.

2cvd__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）22.20 Å
Rg (electron density)20.89 Å
Total Rg21.84 Å
Atom count3409
Residues396
Excluded volume61159 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2cvd__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2cvd__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 (6)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2cvda1
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_idd2cvda2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain
Domain ID domain_idd2cvdb1
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_idd2cvdb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain
Domain ID domain_idd2cvdc1
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_idd2cvdc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain
Domain ID domain_idd2cvdd1
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_idd2cvdd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id2cvdA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2cvdA02
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_id2cvdB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2cvdB02
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_id2cvdC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2cvdC02
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_id2cvdD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2cvdD02
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)