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- PDB-1bh0: STRUCTURE OF A GLUCAGON ANALOG -

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Basic information

Entry
Database: PDB / ID: 1bh0
TitleSTRUCTURE OF A GLUCAGON ANALOG
ComponentsGLUCAGON
KeywordsSYNTHETIC HORMONE
Function / homology
Function and homology information


glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis ...glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / protein kinase A signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / ISOMORPHOUS TO EXISTING NATIVE GLUCAGON STRUCTURE / Resolution: 3 Å
AuthorsSturm, N.S. / Lin, Y. / Burley, S.K. / Krstenansky, J.L. / Ahn, J.-M. / Azizeh, B.Y. / Trivedi, D. / Hruby, V.J.
CitationJournal: J.Med.Chem. / Year: 1998
Title: Structure-function studies on positions 17, 18, and 21 replacement analogues of glucagon: the importance of charged residues and salt bridges in glucagon biological activity.
Authors: Sturm, N.S. / Lin, Y. / Burley, S.K. / Krstenansky, J.L. / Ahn, J.M. / Azizeh, B.Y. / Trivedi, D. / Hruby, V.J.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCAGON


Theoretical massNumber of molelcules
Total (without water)3,4451
Polymers3,4451
Non-polymers00
Water00
1
A: GLUCAGON

A: GLUCAGON

A: GLUCAGON


Theoretical massNumber of molelcules
Total (without water)10,3343
Polymers10,3343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
Unit cell
Length a, b, c (Å)47.900, 47.900, 47.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein/peptide GLUCAGON


Mass: 3444.780 Da / Num. of mol.: 1 / Mutation: R17K, R18K, D21E / Source method: obtained synthetically / Details: SOLID PHASE PEPTIDE SYNTHESIS / References: UniProt: P01275

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growMethod: slow cooling of saturated soln
Details: SLOW COOLING OF HEATED SUPERSATURATED SOLUTION, slow cooling of saturated soln
Crystal grow
*PLUS
Temperature: 50 ℃ / pH: 9.24 / Method: batch method / Details: cooled down from 50degree
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
20.2 Mphosphate11
1protein114.40mg

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 1, 1985
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Observed criterion σ(I): 2 / Redundancy: 1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS TO EXISTING NATIVE GLUCAGON STRUCTURE
Resolution: 3→6 Å / σ(F): 2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms242 0 0 0 242
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg3.3

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