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- PDB-8cks: Crystal structure of Human Serum Albumin in complex with FESAN -

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Basic information

Entry
Database: PDB / ID: 8cks
TitleCrystal structure of Human Serum Albumin in complex with FESAN
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
MYRISTIC ACID / OCTANOIC ACID (CAPRYLIC ACID) / Chem-UZC / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDolot, R.M. / Kaniowski, D. / Ebenryter-Olbinska, K. / Szczupak, P. / Suwara, J. / Nawrot, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Human Serum Albumin in complex with FESAN
Authors: Kaniowski, D. / Ebenryter-Olbinska, K. / Dolot, R.M. / Suwara, J. / Szczupak, P. / Nawrot, B.C.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,62015
Polymers66,5711
Non-polymers2,04914
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-38 kcal/mol
Surface area27560 Å2
Unit cell
Length a, b, c (Å)94.668, 57.817, 129.361
Angle α, β, γ (deg.)90.000, 109.225, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768

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Non-polymers , 7 types, 156 molecules

#2: Chemical ChemComp-UZC / 3,3'-commo-bis(1,2-dicarba-3-ferra-closo-dodecaborane)


Mass: 298.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4B18Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H16O2
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: prism
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 1.4 M (NH4)2SO4, 1% v/v 1,1,1,3,3,3-hexafluoro-2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.6→19.571 Å / Num. obs: 20485 / % possible obs: 99.6 % / Redundancy: 9.7 % / Biso Wilson estimate: 48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.035 / Rrim(I) all: 0.108 / Χ2: 1.1 / Net I/σ(I): 13.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2481 / CC1/2: 0.933 / Rpim(I) all: 0.26 / Rrim(I) all: 0.835 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrysalisPro42.80adata reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.571 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.885 / SU B: 19.706 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.43
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3139 994 4.998 %
Rwork0.2344 18895 -
all0.238 --
obs-19889 96.6 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 71.525 Å2
Baniso -1Baniso -2Baniso -3
1-2.167 Å20 Å23.367 Å2
2---6.392 Å2-0 Å2
3---1.509 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 135 142 4929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124921
X-RAY DIFFRACTIONr_bond_other_d0.0030.0164661
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.6586534
X-RAY DIFFRACTIONr_angle_other_deg0.41.58810878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.631524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5610879
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.8510227
X-RAY DIFFRACTIONr_chiral_restr0.0550.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021023
X-RAY DIFFRACTIONr_nbd_refined0.240.21408
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.24613
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3190.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.227
X-RAY DIFFRACTIONr_nbd_other0.2270.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.24
X-RAY DIFFRACTIONr_mcbond_it5.0687.2152349
X-RAY DIFFRACTIONr_mcbond_other5.0687.2152349
X-RAY DIFFRACTIONr_mcangle_it7.61112.9632938
X-RAY DIFFRACTIONr_mcangle_other7.6112.9652939
X-RAY DIFFRACTIONr_scbond_it5.3027.7122572
X-RAY DIFFRACTIONr_scbond_other5.1967.7132557
X-RAY DIFFRACTIONr_scangle_it8.36913.9673596
X-RAY DIFFRACTIONr_scangle_other8.3313.9743573
X-RAY DIFFRACTIONr_lrange_it11.29668.5685742
X-RAY DIFFRACTIONr_lrange_other11.29568.5685743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.6-2.6660.396630.32713710.3314800.8610.92496.89190.298
2.666-2.7380.383830.3412930.34314340.8990.92295.95540.314
2.738-2.8160.472660.3612790.36614080.8530.91995.52560.322
2.816-2.9010.473610.32612740.33213860.8690.93396.32040.291
2.901-2.9930.436660.30312090.31113300.8650.94295.86470.273
2.993-3.0960.35650.29711460.312760.9160.93994.9060.268
3.096-3.210.347580.26311590.26812560.9270.95696.89490.243
3.21-3.3370.323630.2510740.25411820.9370.96296.19290.232
3.337-3.4810.306540.24110420.24511490.9280.96495.38730.228
3.481-3.6450.341530.24510430.24911180.920.9698.03220.234
3.645-3.8350.405470.2499860.25510660.8940.96296.90430.236
3.835-4.0580.279450.1949160.1989880.950.97697.26720.187
4.058-4.3250.24480.1828710.1859430.9630.97897.45490.177
4.325-4.6520.258520.1828050.1868770.9520.97897.71950.18
4.652-5.0680.244330.2017820.2038290.9620.97598.31120.198
5.068-5.6190.329370.2256940.2317420.9540.97198.51750.223
5.619-6.4010.262350.2316380.2336800.9590.96798.97060.23
6.401-7.6380.326330.2235350.2295740.9530.96898.95470.219
7.638-10.0620.211220.1744590.1764830.9730.98199.58590.182
10.062-19.5710.295100.2363190.2383300.9410.96499.6970.247

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