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- PDB-7qfe: Crystal structure of Human Serum albumin in complex with Gemfibrozil -

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Basic information

Entry
Database: PDB / ID: 7qfe
TitleCrystal structure of Human Serum albumin in complex with Gemfibrozil
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / human serum albumin
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / 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
Chem-4TX / MYRISTIC ACID / TRIETHYLENE GLYCOL / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiberi, S. / Moro, G. / Angelini, A. / Cendron, L.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural Analysis of Human Serum Albumin in Complex with the Fibrate Drug Gemfibrozil.
Authors: Liberi, S. / Linciano, S. / Moro, G. / De Toni, L. / Cendron, L. / Angelini, A.
History
DepositionDec 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)68,67714
Polymers66,5711
Non-polymers2,10613
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-69 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.897, 38.642, 96.213
Angle α, β, γ (deg.)90.000, 104.580, 90.000
Int Tables number5
Space group name H-MC121

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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 genetically manipulated source
Details: missing residues are not visible in the electron density maps
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768

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Non-polymers , 7 types, 81 molecules

#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-4TX / 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid


Mass: 250.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 mM Diethylene glycol, 30 mM triethylene glycol,30 mM Tetraethylene glycol, 30 mM Pentaethylene glycol, 50 mM Bicine, 50 mM Tris, pH 8.5, 12.%%MPD, 12.5 % PEG1000, 12.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.2→46.6 Å / Num. obs: 33831 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2911 / CC1/2: 0.752 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AAE

7aae


Resolution: 2.2→46.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.758 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 3419 10.1 %RANDOM
Rwork0.2194 ---
obs0.223 30407 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.08 Å2 / Biso mean: 56.238 Å2 / Biso min: 23.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.12 Å2
2--3.88 Å20 Å2
3----3.05 Å2
Refinement stepCycle: final / Resolution: 2.2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4626 0 144 68 4838
Biso mean--50.53 48.69 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124866
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.666560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02123.468248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40215872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4871524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023573
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 249 -
Rwork0.315 2227 -
all-2476 -
obs--98.25 %

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