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- PDB-6ins: X-RAY ANALYSIS OF THE SINGLE CHAIN B29-A1 PEPTIDE-LINKED INSULIN ... -

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Basic information

Entry
Database: PDB / ID: 6ins
TitleX-RAY ANALYSIS OF THE SINGLE CHAIN B29-A1 PEPTIDE-LINKED INSULIN MOLECULE. A COMPLETELY INACTIVE ANALOGUE
ComponentsINSULIN
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 D-glucose import / positive regulation of protein secretion / 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-like, subunit E / Insulin-like / 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 ...Insulin-like, subunit E / Insulin-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDerewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Bing, X. / Markussen, J.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: X-ray analysis of the single chain B29-A1 peptide-linked insulin molecule. A completely inactive analogue.
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Bing, X. / Markussen, J.
History
DepositionNov 25, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: INSULIN
F: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5284
Polymers11,3972
Non-polymers1312
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area6180 Å2
MethodPISA
2
E: INSULIN
F: INSULIN
hetero molecules

E: INSULIN
F: INSULIN
hetero molecules

E: INSULIN
F: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,58412
Polymers34,1916
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8630 Å2
ΔGint-171 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.220, 79.220, 37.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11E-30-

ZN

21F-30-

ZN

31E-31-

HOH

41E-69-

HOH

51E-70-

HOH

61E-102-

HOH

71F-81-

HOH

81F-85-

HOH

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Components

#1: Protein/peptide INSULIN


Mass: 5698.532 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details6INS ALTHOUGH THE CRYSTALLIZATION RECIPE FOR 4ZN INSULIN WAS 6INS FOLLOWED, ONLY 2 ZINC IONS WERE ...6INS ALTHOUGH THE CRYSTALLIZATION RECIPE FOR 4ZN INSULIN WAS 6INS FOLLOWED, ONLY 2 ZINC IONS WERE FOUND PER INSULIN HEXAMER. 6INS THE OFF-AXIAL ZINC SITES IN MOLECULE 2 ARE OCCUPIED BY 6INS WATER. 6INS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.51 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
20.1 Mchloride11
1citrate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

SoftwareName: PROLSQ / Version: 6INS / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 2 Å / σ(F): 0
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms788 0 2 179 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0550.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0690.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1580.12
X-RAY DIFFRACTIONp_singtor_nbd0.20.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3650.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.220
X-RAY DIFFRACTIONp_staggered_tor25.820
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / Rfactor all: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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