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9j3p

Human Pigment Epithelium-Derived Factor with Zinc Ions Crystallized in P2(1)2(1)2(1) Space Group

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

Pigment epithelium-derived factor

Homo sapiens

UniProt P36955

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ZINC ION × 1 SULFATE ION × 1 2-(2-METHOXYETHOXY)ETHANOL × 2 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 SULFATE ION × 2 2-(2-METHOXYETHOXY)ETHANOL × 3 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ZINC ION × 2 SULFATE ION × 3 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ZINC ION × 1 SULFATE ION × 2 2-(2-METHOXYETHOXY)ETHANOL × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 ZINC ION × 3 SULFATE ION × 1 2-(2-METHOXYETHOXY)ETHANOL × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1imv 9j3p 9j3p 9j3p 9j3p 9j3p 9j3q

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name PEDF_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–398； UniProt 21–418 Author chain B； PDBConstruct 1–398； UniProt 21–418 Author chain C； PDBConstruct 1–398； UniProt 21–418 Author chain D； PDBConstruct 1–398； UniProt 21–418 Author chain E； PDBConstruct 1–398； UniProt 21–418

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_id9j3p
Deposition date deposition_date2024-08-08
Structure title titleHuman Pigment Epithelium-Derived Factor with Zinc Ions Crystallized in P2(1)2(1)2(1) Space Group
Keywords keywordsmetal-binding protein, signaling protein, neurotrophic factor, anti-tumorigenic factor; SIGNALING PROTEIN
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.

9j3p__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9j3p__assembly_5__model_1 | I(q)

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

9j3p__assembly_5__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）22.47 Å
Rg (electron density)21.35 Å
Total Rg22.39 Å
Atom count5714
Residues368
Excluded volume51443 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9j3p__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9j3p__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9j3p__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9j3p__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 9j3p__assembly_5__model_1 monomeric （1） 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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7. Citations (1)