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- PDB-1dei: DESHEPTAPEPTIDE (B24-B30) INSULIN -

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Basic information

Entry
Database: PDB / ID: 1dei
TitleDESHEPTAPEPTIDE (B24-B30) INSULIN
Components(INSULIN) x 2
KeywordsHORMONE / GLUCOSE METABOLISM
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process ...positive regulation of lipoprotein lipase activity / Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of DNA replication / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / wound healing / hormone activity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBao, S.-J. / Chang, W.-R. / Wan, Z.-L. / Zhang, J.-P. / Liang, D.-C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of desheptapeptide(B24-B30)insulin at 1.6 A resolution: implications for receptor binding.
Authors: Bao, S.J. / Xie, D.L. / Zhang, J.P. / Chang, W.R. / Liang, D.C.
#1: Journal: Sci.Sin., Ser.B (Engl.Ed.) / Year: 1987
Title: Refinement of the Structure of Despentapeptide (B26-B30) Insulin at 1.5 Angstroms Resolution
Authors: Dai, J.B. / Lou, M.Z. / You, J.M. / Liang, D.C.
#2: Journal: Sci.Sin., Ser.B (Engl.Ed.) / Year: 1982
Title: Crystallographic Studies on Desheptapeptide(B24-B30) Insulin-Growth of Single Crystals and Determination of its Crystallographic Parameters
Authors: Chang, W.R. / Xie, D.L. / Liang, D.C. / al., et
History
DepositionMay 15, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN


Theoretical massNumber of molelcules
Total (without water)9,8634
Polymers9,8634
Non-polymers00
Water1,53185
1
A: INSULIN
B: INSULIN


Theoretical massNumber of molelcules
Total (without water)4,9322
Polymers4,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-13 kcal/mol
Surface area3700 Å2
MethodPISA
2
C: INSULIN
D: INSULIN


Theoretical massNumber of molelcules
Total (without water)4,9322
Polymers4,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-13 kcal/mol
Surface area3600 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-37 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.400, 56.300, 23.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MOLECULES EACH CONSISTING OF TWO CHAINS. THIS ENTRY PRESENTS COORDINATES FOR MOLECULES I (CHAIN IDENTIFIERS *A* AND *B*) AND II (CHAIN IDENTIFIERS *C* AND *D*).

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Components

#1: Protein/peptide INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Mutation: CHAIN B, DEL(24-30)
Source method: isolated from a genetically manipulated source
Details: DESHEPTAPEPTIDE (B24-B30) / Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#2: Protein/peptide INSULIN


Mass: 2547.929 Da / Num. of mol.: 2 / Mutation: CHAIN B, DEL(24-30)
Source method: isolated from a genetically manipulated source
Details: DESHEPTAPEPTIDE (B24-B30) / Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 35 %
Crystal grow
*PLUS
Method: other / Details: Chang, W.R., (1982) Sci. Sin. Ser. B, 25, 385.

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Data collection

DiffractionMean temperature: 293.1 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: STOE / Detector: DIFFRACTOMETER / Date: May 11, 1985
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→8 Å / Num. obs: 8331 / % possible obs: 81.1 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 1.6→1.63 Å / % possible all: 44.8

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Processing

Software
NameClassification
PROTEINdata collection
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DESPENTAPEPTIDE(B26-B30)INSULIN

Resolution: 1.6→8 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.215 884 10 %RANDOM
Rwork0.196 ---
obs0.196 8331 81.1 %-
Displacement parametersBiso mean: 14.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 0 85 767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.63 Å
RfactorNum. reflection% reflection
Rfree0.314 24 10 %
Rwork0.26 200 -
obs--40 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rwork: 0.26

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