SAXSdb — 6nug

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

Granulin-4

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 284–307	Fragment：residues 284-307	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；290 K；Pressure 1 NMR sample composition：0.5 mM hGRNA4-28_3s, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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.

Other PDB	Difference from Current Entry 6NUG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G26 THE SOLUTION STRUCTURE OF A WELL-FOLDED PEPTIDE BASED ON THE 31-RESIDUE AMINO-TERMINAL SUBDOMAIN OF HUMAN GRANULIN A Deposited 2000-10-17	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–311（31 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-31)	Mutation：D1V, K3H, S9I, Q20P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Pressure ambient NMR measurement conditions pH 5；298 K；Pressure ambient NMR sample composition 0.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 10% D2O, 90% H2O \| 10% D2O, 90% H2O NMR sample composition 0.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 100% D2O \| 100% D2O	Resolution not provided
2JYE Human Granulin A Deposited 2007-12-13	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–337（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 100% D2O \| 100% D2O	Resolution not provided
2JYT Human Granulin C, isomer 1 Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–417（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 100% D2O \| 100% D2O	Resolution not provided
2JYU Human Granulin C, isomer 2 Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–417（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 100% D2O \| 100% D2O	Resolution not provided
2JYV Human Granulin F Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 123–179（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM [U-100% 15N] HgrnF, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM [U-100% 15N] HgrnF, 100% D2O \| 100% D2O	Resolution not provided
8T8R Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 578–593（16 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20.00 %w/ PEG 3350, 0.20 M Sodium citrate	Resolution 2.87 Å R-free 0.287
8T8S Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 578–593（16 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.10 M Tris, 30.00 %w/v PEG 3000, 0.20 M NaCl	Resolution 2.99 Å R-free 0.275
8T8S Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 578–593（16 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.10 M Tris, 30.00 %w/v PEG 3000, 0.20 M NaCl	Resolution 2.99 Å R-free 0.275

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GRN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–24； UniProt 284–307

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_id	6nug
Deposition date deposition_date	2019-02-01
Structure title title	hGRNA4-28_3s
Keywords keywords	Wound healing agent, CYTOKINE; CYTOKINE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	8.72 Å
Radius of gyration Rg (electron density) rg_electron	8.90 Å
Forward intensity I(0) i0	54674400.00
Molecular weight molecular_weight	51379.0 kDa
Excluded volume excluded_volume	59822 Å³
Envelope volume envelope_volume	6986 Å³
Hydration-shell volume shell_volume	6346 Å³
Envelope diameter envelope_diameter	35.2 Å
Shell Rg shell_rg	14.94 Å
Envelope Rg envelope_rg	10.53 Å
Shape Rg shape_rg	8.94 Å
Total Rg total_rg	9.02 Å
Total atoms total_atoms	6360
Residues n_residues	480
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	30.5 Å
Rg (real space) rg_real	8.76 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	5.4670e+07
I(0) uncertainty (real space) i0_real_error	5.3770e+05
Rg (reciprocal space) rg_reciprocal	8.76 Å
I(0) (reciprocal space) i0_reciprocal	54670000.0000
Solution quality estimate total_estimate	0.8696
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	9.3 Å
Skewness Skewness skewness	0.308
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4448.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 0.921

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Granulin-4
Molecular weight formula_weight	2589.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6360

fit	/app/data/saxs_computation/nu/6nug/6nug.fit
pddf	/app/data/pr_computation/nu/6nug/6nug.pr.out
profile	/app/data/saxs_computation/nu/6nug/6nug.dat

hGRNA4-28_3s

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

Granulin-4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)