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- PDB-7rkd: X-Ray structure of Insulin Analog GLULISINE -

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Basic information

Entry
Database: PDB / ID: 7rkd
TitleX-Ray structure of Insulin Analog GLULISINE
Components
  • Insulin B chain analog
  • Insulin chain A
KeywordsHORMONE / biopharmaceutical compounds
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsReyes-Grajeda, J.P.
CitationJournal: To Be Published
Title: Insulin ANALOGS
Authors: Reyes-Grajeda, J.P.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin chain A
B: Insulin B chain analog
C: Insulin chain A
D: Insulin B chain analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7966
Polymers11,6654
Non-polymers1312
Water84747
1
A: Insulin chain A
B: Insulin B chain analog
C: Insulin chain A
D: Insulin B chain analog
hetero molecules

A: Insulin chain A
B: Insulin B chain analog
C: Insulin chain A
D: Insulin B chain analog
hetero molecules

A: Insulin chain A
B: Insulin B chain analog
C: Insulin chain A
D: Insulin B chain analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38818
Polymers34,99612
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19990 Å2
ΔGint-267 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.945, 81.945, 33.468
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21D-101-

ZN

31D-216-

HOH

41D-218-

HOH

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Components

#1: Protein/peptide Insulin chain A


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain analog


Mass: 3448.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 293.15 K / Method: microbatch / Details: 0.1 M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→40.9793 Å / Num. obs: 23171 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.036 / Rrim(I) all: 0.079 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2% possible allRmerge(I) obsRpim(I) allRrim(I) all
1.25-1.273.511370.13399.9
6.85-40.975.41380.98899.80.0510.0240.057

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
TRUNCATE1.17.29data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O17

6o17


Resolution: 1.25→40.97 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.258 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 2397 10.3 %RANDOM
Rwork0.1939 ---
obs0.196 20773 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 97.73 Å2 / Biso mean: 23.12 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.25→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 2 47 845
Biso mean--60.96 30.79 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.012853
X-RAY DIFFRACTIONr_angle_refined_deg2.9831.6331165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0345107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72823.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60815138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.344153
X-RAY DIFFRACTIONr_chiral_restr0.1780.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02663
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.381 207 -
Rwork0.381 1517 -
obs--99.88 %

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