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1pmx

INSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE

Method: SOLUTION NMR Dmax: 56.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Insulin-like growth factor IB

Homo sapiens

UniProt P05019

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 49–118 Not recorded IGF-1 ANTAGONIST F1-1 × 1 SOLUTION NMR NMR measurement conditions：pH 5.1；313 K；Ionic strength (raw mmCIF value) 25 mM；Pressure 1 NMR sample composition：1.4 MM IGF-I (15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE NMR sample composition：1.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE NMR sample composition：1.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE | 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 1PMX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BQT THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES Deposited 1998-08-18 Different oligomeric state Different experimental conditions 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
NMR measurement conditions pH 3；313 K；Pressure 1
NMR sample composition H2O/D2O=9/1 CONTAINING 10 ACETIC ACID-D4
Resolution not provided
1WQJ Structural Basis for the Regulation of Insulin-Like Growth Factors (IGFs) by IGF Binding Proteins (IGFBPs) Deposited 2004-09-29 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 49–118（70 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；23% PEG 1500, 25mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.255
2DSP Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 49–118（70 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；23% PEG 1500, 25mM Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 2.50 Å R-free 0.271
2DSQ Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 49–118（70 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；290 K；20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 2.80 Å R-free 0.357
2DSQ Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 49–118（70 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；290 K；20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 2.80 Å R-free 0.357
2DSR Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 49–118（70 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；1M lithium sulfate monohydrate, 2% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 2.10 Å R-free 0.256
3LRI Solution structure and backbone dynamics of long-[Arg(3)]insulin-like growth factor-I Deposited 1999-04-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–102（70 aa）
Mutation：E3R, 13 RESIDUE N-TERMINAL EXTENSION No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；303 K；Pressure 1
Resolution not provided
4XSS Insulin-like growth factor I in complex with site 1 of a hybrid insulin receptor / Type 1 insulin-like growth factor receptor Deposited 2015-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 49–118（70 aa） Fragment：UNP residues 49-118
Not recorded SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；1.75 M ammonium sulfate, 0.1 M CAPS-NaOH (pH 10.5), 0.2 M LiSO4
Resolution 3.00 Å R-free 0.229
4XSS Insulin-like growth factor I in complex with site 1 of a hybrid insulin receptor / Type 1 insulin-like growth factor receptor Deposited 2015-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 49–118（70 aa） Fragment：UNP residues 49-118
Not recorded SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；1.75 M ammonium sulfate, 0.1 M CAPS-NaOH (pH 10.5), 0.2 M LiSO4
Resolution 3.00 Å R-free 0.229
5U8Q Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor in complex with IGF-I Deposited 2016-12-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain B 49–118（70 aa）
Not recorded SO4 SULFATE ION × 4 MLT D-MALATE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.2 M ammonium sulfate, 0.1 M imidazole-malate pH 7.0. IGF-1 was included by soaking directly into the mother crystal. For full details see the primary citation.
Resolution 3.27 Å R-free 0.303
6FF3 Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I Deposited 2018-01-03 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 49–118（70 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
6PYH Cryo-EM structure of full-length IGF1R-IGF1 complex. Only the extracellular region of the complex is resolved. Deposited 2019-07-29 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 49–118（70 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6RVA STRUCTURE OF [ASP58]-IGF-I ANALOGUE Deposited 2019-05-31 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 48–118（71 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；313.15 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.18 mM [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 100% D2O | 100% D2O
Resolution not provided
7S0Q Head region of a complex of IGF-I with the ectodomain of a hybrid insulin receptor / type 1 insulin-like growth factor receptor Deposited 2021-08-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 49–118（70 aa）
Not recorded BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Tris pH 8.0 160mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7WRQ Structure of Human IGF1/IGFBP3/ALS Ternary Complex Deposited 2022-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 33–102（70 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging
Resolution 3.60 Å
7YRR Cryo-EM structure of IGF1R with two IGF1 complex Deposited 2022-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 36–95（60 aa）
Chain D 36–95（60 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.30 Å
8EYR Cryo-EM structure of two IGF1 bound full-length mouse IGF1R mutant (four glycine residues inserted in the alpha-CT; IGF1R-P674G4): symmetric conformation Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–195（195 aa）
Chain D 1–195（195 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
8X06 Cryo-EM structure of the IR/IGF-I complex, conformation 1 Deposited 2023-11-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
8X2M Cryo-EM structure of the IR/IGF-I complex, conformation 2 Deposited 2023-11-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Chain E 1–195（195 aa）
Chain F 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8XJS Cryo-EM structure of human insulin receptor bound to 3 IGF-I Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Chain E 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
8XK1 Cryo-EM structure of human insulin receptor bound to 4 IGF-I Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Chain E 1–195（195 aa）
Chain F 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8XKM Cryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 3 Deposited 2023-12-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Chain E 1–195（195 aa）
Chain F 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
8XKR Cryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 2 Deposited 2023-12-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–195（195 aa）
Chain D 1–195（195 aa）
Chain E 1–195（195 aa）
Chain F 1–195（195 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGF1B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–70； UniProt 49–118

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1pmx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pmx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pmx
Deposition date deposition_date2003-06-11
Structure title titleINSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE
Keywords keywordsIGF-I, PEPTIDE BINDING, HIGH AFFINITY LIGAND, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.87 Å
Radius of gyration Rg (electron density) rg_electron14.48 Å
Forward intensity I(0) i0580699000.00
Molecular weight molecular_weight190680.0 kDa
Excluded volume excluded_volume233590 ų
Envelope volume envelope_volume37289 ų
Hydration-shell volume shell_volume16768 ų
Envelope diameter envelope_diameter61.9 Å
Shell Rg shell_rg24.91 Å
Envelope Rg envelope_rg19.80 Å
Shape Rg shape_rg14.49 Å
Total Rg total_rg14.72 Å
Total atoms total_atoms26020
Residues n_residues1720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax56.8 Å
Rg (real space) rg_real14.96 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real5.8070e+08
I(0) uncertainty (real space) i0_real_error6.6520e+06
Rg (reciprocal space) rg_reciprocal14.95 Å
I(0) (reciprocal space) i0_reciprocal580700000.0000
Solution quality estimate total_estimate0.7125
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.6 Å
Skewness Skewness skewness0.509
Kurtosis Kurtosis kurtosis0.026
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha203000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.525; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pmxa_
Class classg — Small proteins
Fold Fold foldg.1 — Insulin-like
Superfamily Superfamily superfamilyg.1.1 — Insulin-like
Family Family familyg.1.1.1 — Insulin-like

CATH v4.4 (1 domains)

Domain ID domain_id1pmxA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology100 — Insulin-like, subunit E
Homologous superfamily homologous superfamily10 — Insulin-like
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8. Citations (2)

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9. Files and Curves (10)