SAXSdb — 1h59

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

INSULIN-LIKE GROWTH FACTOR IA

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 49–118	Fragment：RESIDUES 49-118	INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5 × 3 （P24593）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.60	Resolution 2.10 Å R-free 0.262

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 1H59	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B9G INSULIN-LIKE-GROWTH-FACTOR-1 Deposited 1999-02-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–57（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 1.9；293 K	Resolution not provided
1GZR Human Insulin-like growth factor; ESRF data Deposited 2002-05-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–118（70 aa）	Not recorded	C15 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.	Resolution 2.00 Å R-free 0.295
1GZY Human Insulin-like growth factor; In-house data Deposited 2002-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–118（70 aa）	Not recorded	C15 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.	Resolution 2.54 Å R-free 0.265
1GZZ Human Insulin-like growth factor; Hamburg data Deposited 2002-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–118（70 aa）	Not recorded	C15 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.	Resolution 2.30 Å R-free 0.275
1H02 Human Insulin-like growth factor; SRS Daresbury data Deposited 2002-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–118（70 aa）	Not recorded	C15 N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT.	Resolution 2.00 Å R-free 0.300
1IMX 1.8 Angstrom crystal structure of IGF-1 Deposited 2001-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–118（70 aa）	Not recorded	BR BROMIDE ION × 1 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350, deoxy big CHAPS, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.82 Å R-free 0.258
1TGR Crystal Structure of mini-IGF-1(2) Deposited 2004-05-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–77（29 aa） Fragment：residues 1-52 Chain A 90–110（21 aa） Fragment：residues 1-52	Mutation：T29K Mutation：T29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.65；289 K；Citrate, ethanol, pH 6.65, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.42 Å R-free 0.224
1TGR Crystal Structure of mini-IGF-1(2) Deposited 2004-05-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–77（29 aa） Fragment：residues 1-52 Chain B 90–110（21 aa） Fragment：residues 1-52	Mutation：T29K Mutation：T29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.65；289 K；Citrate, ethanol, pH 6.65, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.42 Å R-free 0.224
1TGR Crystal Structure of mini-IGF-1(2) Deposited 2004-05-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 49–77（29 aa） Fragment：residues 1-52 Chain A 90–110（21 aa） Fragment：residues 1-52 Chain B 49–77（29 aa） Fragment：residues 1-52 Chain B 90–110（21 aa） Fragment：residues 1-52	Mutation：T29K Mutation：T29K Mutation：T29K Mutation：T29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.65；289 K；Citrate, ethanol, pH 6.65, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.42 Å R-free 0.224
2GF1 SOLUTION STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR 1: A NUCLEAR MAGNETIC RESONANCE AND RESTRAINED MOLECULAR DYNAMICS STUDY Deposited 1991-01-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–118（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
3GF1 SOLUTION STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR 1: A NUCLEAR MAGNETIC RESONANCE AND RESTRAINED MOLECULAR DYNAMICS STUDY Deposited 1991-01-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–118（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGFA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 49–118

INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5

OrganismNot specified

UniProt P24593

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 B； UniProt 59–112	Fragment：N-TERMINAL IGF BINDING DOMAIN RESIDUE 58-111	INSULIN-LIKE GROWTH FACTOR IA × 3 （P01343）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.60	Resolution 2.10 Å R-free 0.262

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 1H59	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOE STRUCTURE OF THE IGF BINDING DOMAIN OF THE INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN-5 (IGFBP-5): IMPLICATIONS FOR IGF AND IGF-I RECEPTOR INTERACTIONS Deposited 1998-07-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–106（47 aa） Fragment：BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Pressure 1	Resolution not provided
7UFG Cryo-EM structure of PAPP-A in complex with IGFBP5 Deposited 2022-03-22	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 × 4 PDB declaration: tetrameric	Chain C 21–272（252 aa） Chain D 21–272（252 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；BTP (Bis-Tris-Propane) pH 9.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å

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

View Construct and Data Evidence

UniProt name	IBP5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–54； UniProt 59–112

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	1h59
Deposition date deposition_date	2001-05-21
Structure title title	Complex of IGFBP-5 with IGF-I
Keywords keywords	INSULIN, INSULIN-LIKE GROWTH FACTOR, IGF BINDING PROTEIN; INSULIN
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	14.63 Å
Radius of gyration Rg (electron density) rg_electron	13.51 Å
Forward intensity I(0) i0	2856310.00
Molecular weight molecular_weight	11011.0 kDa
Excluded volume excluded_volume	13474 Å³
Envelope volume envelope_volume	16046 Å³
Hydration-shell volume shell_volume	10423 Å³
Envelope diameter envelope_diameter	45.6 Å
Shell Rg shell_rg	18.75 Å
Envelope Rg envelope_rg	13.75 Å
Shape Rg shape_rg	13.52 Å
Total Rg total_rg	14.61 Å
Total atoms total_atoms	765
Residues n_residues	99
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	46.9 Å
Rg (real space) rg_real	14.57 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	2.8560e+06
I(0) uncertainty (real space) i0_real_error	3.3690e+04
Rg (reciprocal space) rg_reciprocal	14.57 Å
I(0) (reciprocal space) i0_reciprocal	2856000.0000
Solution quality estimate total_estimate	0.9012
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	365400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.990

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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	INSULIN-LIKE GROWTH FACTOR IA
Molecular weight formula_weight	7663.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	809

GPETLCGAELVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCAPLKPAKSA

Entity 2 Entity 2 polymer

Description description	INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5
Molecular weight formula_weight	6051.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SALAEGQSCGVYTERCAQGLRCLPRQDEEKPLHALLHGRGVCLNEKSYREQVKI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1h59a_
Class class	g — Small proteins
Fold Fold fold	g.1 — Insulin-like
Superfamily Superfamily superfamily	g.1.1 — Insulin-like
Family Family family	g.1.1.1 — Insulin-like

Domain ID domain_id	d1h59b_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

CATH v4.4 (2 domains)

Domain ID domain_id	1h59A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	100 — Insulin-like, subunit E
Homologous superfamily homologous superfamily	10 — Insulin-like

Domain ID domain_id	1h59B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	40 — Omega-AgatoxinV
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	74.385 Å
Unit-cell length b length_b	74.385 Å
Unit-cell length c length_c	74.385 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	16.200 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2620

fit	/app/data/saxs_computation/h5/1h59/1h59.fit
pddf	/app/data/pr_computation/h5/1h59/1h59.pr.out
profile	/app/data/saxs_computation/h5/1h59/1h59.dat

Complex of IGFBP-5 with IGF-I

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

INSULIN-LIKE GROWTH FACTOR IA

State in the Current Structure

Other States of the Same Protein in the Database

INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)