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- PDB-1sdb: PORCINE DESB1-2 DESPENTAPEPTIDE(B26-B30) INSULIN -

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Basic information

Entry
Database: PDB / ID: 1sdb
TitlePORCINE DESB1-2 DESPENTAPEPTIDE(B26-B30) INSULIN
Components(DESB1-2 DESPENTAPEPTIDE (B26-B30) INSULIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


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 ...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 / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / lipid biosynthetic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / 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 glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / 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 / acute-phase response / positive regulation of DNA replication / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / positive regulation of protein localization to nucleus / glucose metabolic process / vasodilation / 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 / Resolution: 1.65 Å
AuthorsLiang, D.-C. / Diao, J.-S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of monomeric porcine DesB1-B2 despentapeptide (B26-B30) insulin at 1.65 A resolution.
Authors: Diao, J.S. / Wan, Z.L. / Chang, W.R. / Liang, D.C.
#1: Journal: Sci.Sin.(Engl.Ed.) / Year: 1987
Title: Refinement of the Structure of Despentapeptide (B26-B30) Insulin at 1.5A Resolution
Authors: Dai, J.B. / Lou, M.Z. / You, J.M. / Liang, D.C.
History
DepositionJan 29, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 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: DESB1-2 DESPENTAPEPTIDE (B26-B30) INSULIN
B: DESB1-2 DESPENTAPEPTIDE (B26-B30) INSULIN


Theoretical massNumber of molelcules
Total (without water)4,9802
Polymers4,9802
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-13 kcal/mol
Surface area3260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.880, 24.500, 28.110
Angle α, β, γ (deg.)90.00, 103.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide DESB1-2 DESPENTAPEPTIDE (B26-B30) INSULIN


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#2: Protein/peptide DESB1-2 DESPENTAPEPTIDE (B26-B30) INSULIN


Mass: 2595.972 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 32 %
Crystal grow
*PLUS
pH: 8.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
20.05 Mcitrate12
30.025 %zinc chloride12
410 %acetone12

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→27.3 Å / Num. obs: 3829 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.0272

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Processing

Software
NameClassification
XENGENdata collection
GPRLSArefinement
XENGENdata reduction
RefinementResolution: 1.65→10 Å / σ(F): 2
Details: THE ELECTRON DENSITY FOR THE DESB1-2 DESPENTAPEPTIDE (B 26 - B 30) INSULIN IS ALMOST COMPLETELY DEFINED WHILE DENSITY FOR THE SIDE CHAIN OF RESIDUE ASN B 3 IS WEAK.
RfactorNum. reflection% reflection
Rfree0.22 -10 %
Rwork0.2026 --
obs-3774 86.4 %
Displacement parametersBiso mean: 20.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms345 0 0 33 378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.015
X-RAY DIFFRACTIONp_angle_d0.0380.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.0361.5
X-RAY DIFFRACTIONp_mcangle_it2.9542
X-RAY DIFFRACTIONp_scbond_it2.5131.5
X-RAY DIFFRACTIONp_scangle_it4.0152
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.3340.2
X-RAY DIFFRACTIONp_singtor_nbd0.1370.15
X-RAY DIFFRACTIONp_multtor_nbd0.1810.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.130.15
X-RAY DIFFRACTIONp_planar_tor4.95
X-RAY DIFFRACTIONp_staggered_tor20.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.115
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rfree: 0.2203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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