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- PDB-1pid: BOVINE DESPENTAPEPTIDE INSULIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1pid
TitleBOVINE DESPENTAPEPTIDE INSULIN
Components(DESPENTAPEPTIDE INSULIN) x 2
KeywordsHORMONE / GLUCOSE METABOLISM
Function / homology
Function and homology information


estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite ...estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite / feeding behavior / response to growth hormone / response to food / positive regulation of peptide hormone secretion / positive regulation of Rho protein signal transduction / protein secretion / response to glucose / negative regulation of lipid catabolic process / positive regulation of protein secretion / insulin receptor binding / response to nutrient levels / hormone activity / positive regulation of insulin secretion / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsHolden, P.H. / Papiz, M. / Dodson, G.G.
Citation
Journal: Proteins / Year: 1997
Title: A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin).
Authors: Brange, J. / Dodson, G.G. / Edwards, D.J. / Holden, P.H. / Whittingham, J.L.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: Molecular Replacement Studies on Crystal Forms of Despentapeptide Insulin
Authors: Bi, R.-C. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Giordano, F. / Reynolds, C.D. / Tolley, S.P.
History
DepositionNov 22, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 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 1.5Oct 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: DESPENTAPEPTIDE INSULIN
B: DESPENTAPEPTIDE INSULIN
C: DESPENTAPEPTIDE INSULIN
D: DESPENTAPEPTIDE INSULIN


Theoretical massNumber of molelcules
Total (without water)10,3644
Polymers10,3644
Non-polymers00
Water1,62190
1
A: DESPENTAPEPTIDE INSULIN
B: DESPENTAPEPTIDE INSULIN


Theoretical massNumber of molelcules
Total (without water)5,1822
Polymers5,1822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DESPENTAPEPTIDE INSULIN
D: DESPENTAPEPTIDE INSULIN


Theoretical massNumber of molelcules
Total (without water)5,1822
Polymers5,1822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.700, 26.180, 51.710
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number5
Space group name H-MC1211
Components on special symmetry positions
IDModelComponents
11B-98-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99439, 0.035258, 0.099728), (-0.045704, 0.993476, 0.10448), (-0.095394, -0.108451, 0.989514)
Vector: -5.47395, -1.22199, 27.14091)

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Components

#1: Protein/peptide DESPENTAPEPTIDE INSULIN


Mass: 2339.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01317
#2: Protein/peptide DESPENTAPEPTIDE INSULIN


Mass: 2842.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01317
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.72 Å3/Da / Density % sol: 28.43 %
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
20.02 MTris-HCl115.0ml
30.05 Mtrisodium citrate115.0ml
440 %satammonium sulfate111.5ml
60.1 Mcitric acid11
1depentapeptide insulin1115 mg
5acetone111.5ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 31367 / % possible obs: 90.7 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.3→25.4 Å / σ(F): 0 /
Num. reflection% reflection
obs16916 90.7 %
Refinement stepCycle: LAST / Resolution: 1.3→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 0 90 820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2593
X-RAY DIFFRACTIONp_mcangle_it2.443.5
X-RAY DIFFRACTIONp_scbond_it4.5273
X-RAY DIFFRACTIONp_scangle_it4.4753.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.080.1
X-RAY DIFFRACTIONp_singtor_nbd0.160.5
X-RAY DIFFRACTIONp_multtor_nbd0.270.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.310.5
X-RAY DIFFRACTIONp_planar_tor2.420
X-RAY DIFFRACTIONp_staggered_tor14.420
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.320
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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