[English] 日本語
- PDB-4p65: Crystal structure of an cyclohexylalanine substituted insulin analog. -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 4p65
TitleCrystal structure of an cyclohexylalanine substituted insulin analog.
Components(Insulin) x 2
KeywordsHORMONE / protein hormone / non-standard mutagenesis
Function / homology
Function and homology information

Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of protein metabolic process => GO:0051247 / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Signal attenuation / negative regulation of protein secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / Regulation of insulin secretion / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / transport vesicle / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of cell differentiation / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / cognition / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / acute-phase response / negative regulation of proteolysis / hormone activity / vasodilation / insulin receptor binding / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / glucose metabolic process / regulation of protein localization / cell-cell signaling / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / protease binding / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription, DNA-templated / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
AuthorsPandyarajan, V. / Wan, Z. / Weiss, M.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Aromatic Anchor at an Invariant Hormone-Receptor Interface: FUNCTION OF INSULIN RESIDUE B24 WITH APPLICATION TO PROTEIN DESIGN.
Authors: Pandyarajan, V. / Smith, B.J. / Phillips, N.B. / Whittaker, L. / Cox, G.P. / Wickramasinghe, N. / Menting, J.G. / Wan, Z.L. / Whittaker, J. / Ismail-Beigi, F. / Lawrence, M.C. / Weiss, M.A.
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references

Structure visualization

Structure viewerMolecule:

Downloads & links


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

Theoretical massNumber of molelcules
Total (without water)35,61822

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-233 kcal/mol
Surface area13380 Å2
Unit cell
Length a, b, c (Å)46.040, 60.900, 59.300
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number4
Space group name H-MP1211


Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin /

Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin /

Mass: 3424.967 Da / Num. of mol.: 6 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

Non-polymers , 4 types, 217 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol

Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride

Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: sodium citrate, phenol, sodium chloride, zinc acetate, tris

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
ReflectionResolution: 1.5→42.3 Å / Num. obs: 54128 / % possible obs: 95.8 % / Redundancy: 1.9 % / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3


SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNJ
Resolution: 1.5→42.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4823 10.01 %random selection
Rwork0.1598 ---
obs0.1641 48189 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 46 207 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012620
X-RAY DIFFRACTIONf_angle_d1.3513522
X-RAY DIFFRACTIONf_dihedral_angle_d14.777980
X-RAY DIFFRACTIONf_chiral_restr0.065383
X-RAY DIFFRACTIONf_plane_restr0.006445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.36171660.33191447X-RAY DIFFRACTION99
1.5171-1.53490.34971600.30431471X-RAY DIFFRACTION100
1.5349-1.55360.2911580.27341420X-RAY DIFFRACTION99
1.5536-1.57330.31111600.26441445X-RAY DIFFRACTION99
1.5733-1.5940.29981660.24371436X-RAY DIFFRACTION100
1.594-1.61580.27211560.22971446X-RAY DIFFRACTION100
1.6158-1.63890.25411590.2161465X-RAY DIFFRACTION100
1.6389-1.66340.23831610.20061417X-RAY DIFFRACTION100
1.6634-1.68940.23991620.17671456X-RAY DIFFRACTION100
1.6894-1.71710.21561700.17991435X-RAY DIFFRACTION100
1.7171-1.74670.22541880.17281423X-RAY DIFFRACTION100
1.7467-1.77840.24551630.1681487X-RAY DIFFRACTION100
1.7784-1.81270.2151540.16831435X-RAY DIFFRACTION100
1.8127-1.84970.22821550.1581466X-RAY DIFFRACTION100
1.8497-1.88990.22331550.15811435X-RAY DIFFRACTION100
1.8899-1.93380.23661710.15611464X-RAY DIFFRACTION100
1.9338-1.98220.20371600.1541456X-RAY DIFFRACTION100
1.9822-2.03580.18221650.14911436X-RAY DIFFRACTION100
2.0358-2.09570.18511720.14041444X-RAY DIFFRACTION100
2.0957-2.16330.19081590.14551452X-RAY DIFFRACTION100
2.1633-2.24060.18531620.1411459X-RAY DIFFRACTION100
2.2406-2.33040.19691540.14341456X-RAY DIFFRACTION100
2.3304-2.43640.19791580.15131481X-RAY DIFFRACTION100
2.4364-2.56480.18171840.13941434X-RAY DIFFRACTION100
2.5648-2.72550.20341340.15281490X-RAY DIFFRACTION100
2.7255-2.93590.19631480.15951466X-RAY DIFFRACTION100
2.9359-3.23130.19671690.16041449X-RAY DIFFRACTION100
3.2313-3.69860.17941580.15091480X-RAY DIFFRACTION99
3.6986-4.65890.1861510.14171439X-RAY DIFFRACTION97
4.6589-42.31630.21241450.17421276X-RAY DIFFRACTION85

About Yorodumi


Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more