2om1

Structure of human insulin in presence of thiocyanate at pH 6.5

Method: X-RAY DIFFRACTION Dmax: 130.3 Å Quality: REASONABLE

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

Insulin A chain

OrganismNot specified

UniProt P01308

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 × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 90–110 Chain B; UniProt 25–54 Chain C; UniProt 90–110 Chain D; UniProt 25–54 Chain E; UniProt 90–110 Chain F; UniProt 25–54 Chain G; UniProt 90–110 Chain H; UniProt 25–54 Chain I; UniProt 90–110 Chain J; UniProt 25–54 Chain K; UniProt 90–110 Chain L; UniProt 25–54 Not recorded RCO RESORCINOL × 6 ZN ZINC ION × 2 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;15mM Na-SCN, 5%(v/v) ethanol, 200mM phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.97 Å R-free 0.212
2 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain 1; UniProt 90–110 Chain 2; UniProt 25–54 Chain 3; UniProt 90–110 Chain 4; UniProt 25–54 Chain Q; UniProt 90–110 Chain R; UniProt 25–54 Chain S; UniProt 90–110 Chain T; UniProt 25–54 Chain U; UniProt 90–110 Chain V; UniProt 25–54 Chain X; UniProt 90–110 Chain Y; UniProt 25–54 Not recorded RCO RESORCINOL × 6 ZN ZINC ION × 2 SCN THIOCYANATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;15mM Na-SCN, 5%(v/v) ethanol, 200mM phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.97 Å R-free 0.212
3 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain a; UniProt 90–110 Chain b; UniProt 25–54 Chain c; UniProt 90–110 Chain d; UniProt 25–54 Chain e; UniProt 90–110 Chain f; UniProt 25–54 Chain g; UniProt 90–110 Chain h; UniProt 25–54 Chain i; UniProt 90–110 Chain j; UniProt 25–54 Chain k; UniProt 90–110 Chain l; UniProt 25–54 Not recorded RCO RESORCINOL × 6 ZN ZINC ION × 2 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;15mM Na-SCN, 5%(v/v) ethanol, 200mM phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 1.97 Å R-free 0.212

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.

369 other PDB entries and 581 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INS_HUMAN
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain 1; PDBConstruct 1–21; UniProt 90–110 Author chain 3; PDBConstruct 1–21; UniProt 90–110 Author chain A; PDBConstruct 1–21; UniProt 90–110 Author chain C; PDBConstruct 1–21; UniProt 90–110 Author chain E; PDBConstruct 1–21; UniProt 90–110 Author chain G; PDBConstruct 1–21; UniProt 90–110 Author chain I; PDBConstruct 1–21; UniProt 90–110 Author chain K; PDBConstruct 1–21; UniProt 90–110 Author chain Q; PDBConstruct 1–21; UniProt 90–110 Author chain S; PDBConstruct 1–21; UniProt 90–110 Author chain U; PDBConstruct 1–21; UniProt 90–110 Author chain X; PDBConstruct 1–21; UniProt 90–110 Author chain a; PDBConstruct 1–21; UniProt 90–110 Author chain c; PDBConstruct 1–21; UniProt 90–110 Author chain e; PDBConstruct 1–21; UniProt 90–110 Author chain g; PDBConstruct 1–21; UniProt 90–110 Author chain i; PDBConstruct 1–21; UniProt 90–110 Author chain k; PDBConstruct 1–21; UniProt 90–110 Author chain 2; PDBConstruct 1–30; UniProt 25–54 Author chain 4; PDBConstruct 1–30; UniProt 25–54 Author chain B; PDBConstruct 1–30; UniProt 25–54 Author chain D; PDBConstruct 1–30; UniProt 25–54 Author chain F; PDBConstruct 1–30; UniProt 25–54 Author chain H; PDBConstruct 1–30; UniProt 25–54 Author chain J; PDBConstruct 1–30; UniProt 25–54 Author chain L; PDBConstruct 1–30; UniProt 25–54 Author chain R; PDBConstruct 1–30; UniProt 25–54 Author chain T; PDBConstruct 1–30; UniProt 25–54 Author chain V; PDBConstruct 1–30; UniProt 25–54 Author chain Y; PDBConstruct 1–30; UniProt 25–54 Author chain b; PDBConstruct 1–30; UniProt 25–54 Author chain d; PDBConstruct 1–30; UniProt 25–54 Author chain f; PDBConstruct 1–30; UniProt 25–54 Author chain h; PDBConstruct 1–30; UniProt 25–54 Author chain j; PDBConstruct 1–30; UniProt 25–54 Author chain l; PDBConstruct 1–30; UniProt 25–54

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 2om1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2om1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2om1
Deposition date deposition_date2007-01-20
Structure title titleStructure of human insulin in presence of thiocyanate at pH 6.5
Keywords keywordsR6 conformation, hormone; HORMONE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.00
Radius of gyration Rg (electron density) rg_electron38.25
Forward intensity I(0) i0174708000.00
Molecular weight molecular_weight105130.0 kDa
Excluded volume excluded_volume130200 ų
Envelope volume envelope_volume166760 ų
Hydration-shell volume shell_volume39018 ų
Envelope diameter envelope_diameter132.6
Shell Rg shell_rg40.70
Envelope Rg envelope_rg38.05
Shape Rg shape_rg38.26
Total Rg total_rg38.37
Total atoms total_atoms7309
Residues n_residues902
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax130.3
Rg (real space) rg_real38.41
Rg uncertainty (real space) rg_real_error1.29
I(0) (real space) i0_real1.7470e+08
I(0) uncertainty (real space) i0_real_error3.2720e+06
Rg (reciprocal space) rg_reciprocal38.16
I(0) (reciprocal space) i0_reciprocal174700000.0000
Solution quality estimate total_estimate0.5674
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.472
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha525600000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.608; Stabil: 1.000; Sysdev: 0.020; Positv: 1.000; Valcen: 0.678; Smooth: 0.813

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd2om121
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om141
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1b1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1d1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1f1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1h1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1j1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1l1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1r1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1t1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1v1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain
Domain ID domain_idd2om1y1
Class classj — Peptides
Fold Fold foldj.75 — Isolated insulin B-chain
Superfamily Superfamily superfamilyj.75.1 — Isolated insulin B-chain
Family Family familyj.75.1.1 — Isolated insulin B-chain

8. Citations (1)

9. Files and Curves (10)