SAXSdb — 6fey

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

Neural/ectodermal development factor IMP-L2

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 26–267 Chain B； UniProt 26–267	Not recorded	Probable insulin-like peptide 5 × 2 （Q7KUD5） Probable insulin-like peptide 5 × 2 （Q7KUD5）	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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 26–267 Chain D； UniProt 26–267	Not recorded	Probable insulin-like peptide 5 × 2 （Q7KUD5） Probable insulin-like peptide 5 × 2 （Q7KUD5）	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

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 6FEY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CBP Crystal structure of neural ectodermal development factor IMP-L2. Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 5–267（263 aa） Chain B 5–267（263 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；HANGING-DROP EXPERIMENTS BY MIXING 1 UL PROTEIN (5.5. MG/ML IN 10 MM HEPES PH 7.4, 20 MM NACL) AND 1 UL RESERVOIR SOLUTION (17% PEG-6000, 0.1 M TRIS HYDROCHLORIDE, PH 7.0)	Resolution 1.60 Å R-free 0.188
6FF3 Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I 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 × 2 PDB declaration: dimeric	Chain A 26–267（242 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5	Resolution 2.57 Å R-free 0.285

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMPL2_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 26–267 Author chain B； PDBConstruct 1–242； UniProt 26–267 Author chain C； PDBConstruct 1–242； UniProt 26–267 Author chain D； PDBConstruct 1–242； UniProt 26–267

Probable insulin-like peptide 5

Drosophila melanogaster

UniProt Q7KUD5

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 84–108 Chain H； UniProt 24–51 Chain I； UniProt 84–108 Chain J； UniProt 24–51	Mutation：K95N	Neural/ectodermal development factor IMP-L2 × 2 （Q09024）	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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain E； UniProt 84–108 Chain F； UniProt 24–51 Chain K； UniProt 84–108 Chain L； UniProt 24–51	Mutation：K95N	Neural/ectodermal development factor IMP-L2 × 2 （Q09024）	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

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 6FEY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WFU Crystal structure of DILP5 variant DB Deposited 2009-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 87–108（22 aa） Fragment：RESIDUES 87-108 Chain B 24–47（24 aa） Fragment：RESIDUES 24-47	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 20% PEG4000	Resolution 1.85 Å R-free 0.256
2WFV Crystal structure of DILP5 variant C4 Deposited 2009-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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
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 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	INSL5_DROME
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain E； PDBConstruct 1–25； UniProt 84–108 Author chain G； PDBConstruct 1–25； UniProt 84–108 Author chain I； PDBConstruct 1–25； UniProt 84–108 Author chain K； PDBConstruct 1–25； UniProt 84–108 Author chain F； PDBConstruct 1–28； UniProt 24–51 Author chain H； PDBConstruct 1–28； UniProt 24–51 Author chain J； PDBConstruct 1–28； UniProt 24–51 Author chain L； PDBConstruct 1–28； UniProt 24–51

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	6fey
Deposition date deposition_date	2018-01-03
Structure title title	Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin
Keywords keywords	insulin, insulin binding protein, Drosophila, imaginal morphogenesis, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING 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	33.27 Å
Radius of gyration Rg (electron density) rg_electron	32.83 Å
Forward intensity I(0) i0	126270000.00
Molecular weight molecular_weight	83077.0 kDa
Excluded volume excluded_volume	101150 Å³
Envelope volume envelope_volume	148360 Å³
Hydration-shell volume shell_volume	38939 Å³
Envelope diameter envelope_diameter	117.4 Å
Shell Rg shell_rg	38.36 Å
Envelope Rg envelope_rg	32.78 Å
Shape Rg shape_rg	32.81 Å
Total Rg total_rg	33.33 Å
Total atoms total_atoms	5819
Residues n_residues	841
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	112.8 Å
Rg (real space) rg_real	33.44 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	1.2630e+08
I(0) uncertainty (real space) i0_real_error	2.1400e+06
Rg (reciprocal space) rg_reciprocal	33.37 Å
I(0) (reciprocal space) i0_reciprocal	126300000.0000
Solution quality estimate total_estimate	0.8650
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.243
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17610000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.840

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neural/ectodermal development factor IMP-L2
Molecular weight formula_weight	27290.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,C
Atom count atom_count	5823

RAVDLVDDSNDVDNSIEAEEEKPRNRAFEADWLKFTKTPPTKLQQADGATIEIVCEMMGSQVPSIQWVVGHLPRSELDDLDSNQVAEEAPSAIVRVRSSHIIDHVLSEARTYTCVGRTGSKTIYASTVVHPPRSSRLTPEKTYPGAQKPRIIYTEKTHLDLMGSNIQLPCRVHARPRAEITWLNNENKEIVQGHRHRVLANGDLLISEIKWEDMGNYKCIARNVVGKDTADTFVYPVLNEED

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Probable insulin-like peptide 5
Molecular weight formula_weight	2795.1 kDa
Mutation mutation	K95N
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,K

DFRGVVDSCCRNSCSFSTLRAYCDS

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 polymer

Description description	Probable insulin-like peptide 5
Molecular weight formula_weight	3018.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H,J,L

NSLRACGPALMDMLRVACPNGFNSMFAK

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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6feyA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6feyA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6feyB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6feyB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	150.834 Å
Unit-cell length b length_b	150.834 Å
Unit-cell length c length_c	125.321 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.480 Å
Low-resolution limit resolution_low	29.600 Å
R factor r_factor	0.2655
R_work r_work	0.2614
R_free r_free	0.3446

fit	/app/data/saxs_computation/fe/6fey/6fey.fit
pddf	/app/data/pr_computation/fe/6fey/6fey.pr.out
profile	/app/data/saxs_computation/fe/6fey/6fey.dat

Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin

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

Neural/ectodermal development factor IMP-L2

State in the Current Structure

Other States of the Same Protein in the Database

Probable insulin-like peptide 5

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)