SAXSdb — 2wfu

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

PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN

DROSOPHILA MELANOGASTER

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 87–108 Chain B； UniProt 24–47	Fragment：RESIDUES 87-108 Mutation：YES Fragment：RESIDUES 24-47	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：20% PEG4000	Resolution 1.85 Å R-free 0.256

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 2WFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WFV Crystal structure of DILP5 variant C4 Deposited 2009-04-15	Different construct Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 84–108（25 aa） Fragment：RESIDUES 84-108 Chain B 24–46（23 aa） Fragment：RESIDUES 24-46	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% PEG4000	Resolution 1.85 Å R-free 0.232
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 84–108（25 aa） Chain H 24–51（28 aa） Chain I 84–108（25 aa） Chain J 24–51（28 aa）	Mutation：K95N Mutation：K95N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5	Resolution 3.48 Å R-free 0.345
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 84–108（25 aa） Chain F 24–51（28 aa） Chain K 84–108（25 aa） Chain L 24–51（28 aa）	Mutation：K95N Mutation：K95N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5	Resolution 3.48 Å R-free 0.345
8CLS Drosophila melanogaster insulin receptor ectodomain in complex with DILP5 Deposited 2023-02-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 84–108（25 aa） Chain D 24–51（28 aa） Chain E 84–108（25 aa） Chain F 24–51（28 aa） Chain G 84–108（25 aa） Chain H 24–51（28 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9EF9 Cryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with three DILP5, asymmetric conformation Deposited 2024-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 84–108（25 aa） Chain D 24–51（28 aa） Chain E 84–108（25 aa） Chain F 24–51（28 aa） Chain G 84–108（25 aa） Chain H 24–51（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	INSL5_DROME
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–22； UniProt 87–108 Author chain B； PDBConstruct 1–24； UniProt 24–47

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	2wfu
Deposition date deposition_date	2009-04-15
Structure title title	Crystal structure of DILP5 variant DB
Keywords keywords	CLEAVAGE ON PAIR OF BASIC RESIDUES, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	11.15 Å
Radius of gyration Rg (electron density) rg_electron	9.61 Å
Forward intensity I(0) i0	737424.00
Molecular weight molecular_weight	4879.0 kDa
Excluded volume excluded_volume	5834 Å³
Envelope volume envelope_volume	6605 Å³
Hydration-shell volume shell_volume	6247 Å³
Envelope diameter envelope_diameter	33.3 Å
Shell Rg shell_rg	14.49 Å
Envelope Rg envelope_rg	10.03 Å
Shape Rg shape_rg	9.63 Å
Total Rg total_rg	10.96 Å
Total atoms total_atoms	334
Residues n_residues	46
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	35.6 Å
Rg (real space) rg_real	11.10 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	7.3740e+05
I(0) uncertainty (real space) i0_real_error	8.1400e+03
Rg (reciprocal space) rg_reciprocal	11.10 Å
I(0) (reciprocal space) i0_reciprocal	737400.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.4 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.328
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60730.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN
Molecular weight formula_weight	2375.6 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	371

GVVDSCCRNSCSFSTLRAYCDS

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	PROBABLE INSULIN-LIKE PEPTIDE 5 B CHAIN
Molecular weight formula_weight	2540.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NSLRACGPALMDMLRVACPNGFNS

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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8. Citations (1)

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Unit-cell length a length_a	39.789 Å
Unit-cell length b length_b	39.789 Å
Unit-cell length c length_c	45.321 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	24.150 Å
R factor r_factor	0.2190
R_work r_work	0.2150
R_free r_free	0.2560

fit	/app/data/saxs_computation/wf/2wfu/2wfu.fit
pddf	/app/data/pr_computation/wf/2wfu/2wfu.pr.out
profile	/app/data/saxs_computation/wf/2wfu/2wfu.dat

Crystal structure of DILP5 variant DB

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

PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)