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- PDB-1ax8: Human obesity protein, leptin -

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Basic information

Entry
Database: PDB / ID: 1ax8
TitleHuman obesity protein, leptin
ComponentsOBESITY PROTEIN
KeywordsCYTOKINE / HELICAL CYTOKINE / HEMATOPOIETIC FACTOR / DIABETES / OBESITY
Function / homology
Function and homology information


regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell mediated cytotoxicity / regulation of natural killer cell proliferation / leptin receptor binding ...regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell mediated cytotoxicity / regulation of natural killer cell proliferation / leptin receptor binding / bone growth / positive regulation of luteinizing hormone secretion / regulation of natural killer cell activation / glycerol biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of hepatic stellate cell activation / positive regulation of follicle-stimulating hormone secretion / regulation of steroid biosynthetic process / positive regulation of monoatomic ion transport / regulation of intestinal cholesterol absorption / regulation of bone remodeling / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of nitric-oxide synthase activity / adult feeding behavior / activation of protein kinase C activity / bone mineralization involved in bone maturation / sexual reproduction / negative regulation of cartilage development / ovulation from ovarian follicle / negative regulation of appetite / positive regulation of developmental growth / leukocyte tethering or rolling / energy reserve metabolic process / bile acid metabolic process / cellular response to leptin stimulus / negative regulation of D-glucose import / prostaglandin secretion / cardiac muscle hypertrophy / Signaling by Leptin / cell surface receptor signaling pathway via STAT / hormone metabolic process / positive regulation of p38MAPK cascade / intestinal absorption / insulin secretion / aorta development / negative regulation of vasoconstriction / regulation of gluconeogenesis / peptide hormone receptor binding / eating behavior / fatty acid beta-oxidation / regulation of cytokine production involved in inflammatory response / central nervous system neuron development / response to dietary excess / negative regulation of lipid storage / T cell differentiation / response to vitamin E / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / positive regulation of TOR signaling / regulation of angiogenesis / adipose tissue development / phagocytosis / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / energy homeostasis / cellular response to retinoic acid / positive regulation of interleukin-12 production / regulation of insulin secretion / negative regulation of autophagy / cholesterol metabolic process / response to activity / positive regulation of interleukin-8 production / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / determination of adult lifespan / response to insulin / placenta development / hormone activity / Transcriptional regulation of white adipocyte differentiation / regulation of blood pressure / lipid metabolic process / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / cellular response to insulin stimulus / glucose metabolic process / circadian rhythm / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / glucose homeostasis / response to estradiol / positive regulation of cold-induced thermogenesis / angiogenesis / response to ethanol / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / regulation of cell cycle
Similarity search - Function
Leptin / Leptin / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsZhang, F. / Beals, J.M. / Briggs, S.L. / Clawson, D.K. / Wery, J.-P. / Schevitz, R.W.
Citation
Journal: Nature / Year: 1997
Title: Crystal structure of the obese protein leptin-E100.
Authors: Zhang, F. / Basinski, M.B. / Beals, J.M. / Briggs, S.L. / Churgay, L.M. / Clawson, D.K. / DiMarchi, R.D. / Furman, T.C. / Hale, J.E. / Hsiung, H.M. / Schoner, B.E. / Smith, D.P. / Zhang, X.Y. ...Authors: Zhang, F. / Basinski, M.B. / Beals, J.M. / Briggs, S.L. / Churgay, L.M. / Clawson, D.K. / DiMarchi, R.D. / Furman, T.C. / Hale, J.E. / Hsiung, H.M. / Schoner, B.E. / Smith, D.P. / Zhang, X.Y. / Wery, J.P. / Schevitz, R.W.
#1: Journal: Nature / Year: 1995
Title: Erratum. Positional Cloning of the Mouse Obese Gene and its Human Homologue
Authors: Zhang, Y. / Proenca, R. / Maffei, M. / Barone, M. / Leopold, L. / Friedman, J.M.
#2: Journal: Nature / Year: 1994
Title: Positional Cloning of the Mouse Obese Gene and its Human Homologue
Authors: Zhang, Y. / Proenca, R. / Maffei, M. / Barone, M. / Leopold, L. / Friedman, J.M.
History
DepositionOct 31, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 9, 2012Group: Derived calculations
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OBESITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,9841
Polymers15,9841
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: OBESITY PROTEIN

A: OBESITY PROTEIN

A: OBESITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,9533
Polymers47,9533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area4040 Å2
ΔGint-34 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.140, 88.140, 48.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein OBESITY PROTEIN / LEPTIN


Mass: 15984.296 Da / Num. of mol.: 1 / Mutation: W100E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: ADIPOSE / Cell line: BL21 / Gene: OBESE GENE / Plasmid: BL21 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P41159
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 65.4 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.8M NA FORMATE, 100MM TRIS, PH 7.5
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 8404 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.052 / Rsym value: 0.054 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 8.5 / Rsym value: 0.263 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 45300
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→8 Å / Rfactor Rfree error: 0.0095 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 877 10.6 %RANDOM
Rwork0.185 ---
obs0.185 8253 99 %-
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--5.74 Å20 Å2
3---0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 0 71 1074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.38
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.342 97 10 %
Rwork0.322 873 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.38
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor obs: 0.322

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