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- PDB-2ws6: Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hex... -

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Basic information

Entry
Database: PDB / ID: 2ws6
TitleSemi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form
Components
  • (INSULIN B CHAIN) x 2
  • INSULIN A CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / ANALOGUE / DIABETES MELLITUS
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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-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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrzozowski, A.M. / Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Implications for the Active Form of Human Insulin Based on the Structural Convergence of Highly Active Hormone Analogues.
Authors: Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. / Brzozowski, A.M.
History
DepositionSep 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
E: INSULIN A CHAIN
F: INSULIN B CHAIN
G: INSULIN A CHAIN
H: INSULIN B CHAIN
I: INSULIN A CHAIN
J: INSULIN B CHAIN
K: INSULIN A CHAIN
L: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82023
Polymers34,96212
Non-polymers85811
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18740 Å2
ΔGint-234.6 kcal/mol
Surface area13550 Å2
MethodPISA
2
C: INSULIN A CHAIN
D: INSULIN B CHAIN
G: INSULIN A CHAIN
H: INSULIN B CHAIN
K: INSULIN A CHAIN
L: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,95612
Polymers17,4816
Non-polymers4756
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-103.4 kcal/mol
Surface area10850 Å2
MethodPISA
3
A: INSULIN A CHAIN
B: INSULIN B CHAIN
E: INSULIN A CHAIN
F: INSULIN B CHAIN
I: INSULIN A CHAIN
J: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,86411
Polymers17,4816
Non-polymers3835
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-104.2 kcal/mol
Surface area10890 Å2
MethodPISA
4
A: INSULIN A CHAIN
B: INSULIN B CHAIN
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8246
Polymers11,6354
Non-polymers1882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-30.3 kcal/mol
Surface area6660 Å2
MethodPISA
5
I: INSULIN A CHAIN
J: INSULIN B CHAIN
K: INSULIN A CHAIN
L: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,14511
Polymers11,6634
Non-polymers4827
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-31.4 kcal/mol
Surface area6710 Å2
MethodPISA
6
E: INSULIN A CHAIN
F: INSULIN B CHAIN
G: INSULIN A CHAIN
H: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8526
Polymers11,6634
Non-polymers1882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-29.8 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.962, 61.927, 47.297
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 3 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: A CHAIN OF HUMAN INSULIN / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#3: Protein/peptide
INSULIN B CHAIN


Mass: 3447.979 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: METHYLATION OF TYROSINE RESIDUE 26 NITROGEN ATOM OF HUMAN INSULIN
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308

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Non-polymers , 5 types, 255 molecules

#4: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsZINC (ZN): ZINC CATION CHLORINE (CL): CHLORINE ANION
Sequence detailsN ATOM OF 26Y PEPTIDE IS METHYLATED

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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: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.2
Details: 6% TRIS PH 8.2, 0.1 M NA CITRATE, 0.02% ZN ACETATE, 0.06% PHENOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 50473 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSO

1mso


Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.533 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. B27-B30, D28-D30 F30, H28-H30, L28-L30 ARE NOT MODELLED DUE TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.19951 2565 5.1 %RANDOM
Rwork0.15002 ---
obs0.15244 47779 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20.17 Å2
2---0.53 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 52 244 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.9553488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96124.531128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5091510
X-RAY DIFFRACTIONr_chiral_restr0.2040.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4751.51544
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.69722485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.87331017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6914.51003
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.04932561
X-RAY DIFFRACTIONr_sphericity_free12.1613249
X-RAY DIFFRACTIONr_sphericity_bonded6.65532486
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 201 -
Rwork0.214 3437 -
obs--98.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2601-0.389-1.120.90560.51112.1288-0.0403-0.26940.21730.04860.0247-0.16170.01540.18190.01550.0230.0085-0.02220.0393-0.01540.081224.7161-0.569611.4187
22.04191.18170.32991.8005-0.1680.3314-0.0151-0.07140.05810.08230.0149-0.042-0.0560.0110.00020.0288-0.0022-0.00770.0173-0.0170.021421.042113.30572.5936
31.22040.8149-0.21511.24940.24160.7338-0.0485-0.0255-0.091-0.0090.005-0.0310.0675-0.03710.04340.0312-0.01180.0050.01710.00630.01118.3512-12.8582.4047
40.339-0.00720.45740.3101-0.4182.0935-0.0224-0.0328-0.00530.0598-0.00920.0328-0.0835-0.0660.03160.01980.00330.00950.0109-0.00490.01164.5798-0.382212.1986
50.7676-0.06270.02870.6362-0.32420.9718-0.02580.0431-0.00380.0026-0.0162-0.0411-0.0080.02660.0420.01870.00220.00030.0064-0.00080.004822.3943-0.4647-10.9004
61.1572-0.6372-0.80751.18220.87861.23470.03440.1269-0.0279-0.0895-0.08110.0185-0.0894-0.09620.04670.0260.009-0.0060.0195-0.00320.00296.36451.7121-10.7011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION1B1 - 26
3X-RAY DIFFRACTION2C1 - 21
4X-RAY DIFFRACTION2D1 - 26
5X-RAY DIFFRACTION3E1 - 21
6X-RAY DIFFRACTION3F1 - 29
7X-RAY DIFFRACTION4G1 - 21
8X-RAY DIFFRACTION4H1 - 27
9X-RAY DIFFRACTION5I1 - 21
10X-RAY DIFFRACTION5J1 - 28
11X-RAY DIFFRACTION6K1 - 21
12X-RAY DIFFRACTION6L1 - 27

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