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- PDB-6xv0: lauric acid functionalized hexamolybdoaluminate bound to human se... -

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Basic information

Entry
Database: PDB / ID: 6xv0
Titlelauric acid functionalized hexamolybdoaluminate bound to human serum albumin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / serum protein / complex / polyoxometalate
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
lauric acid functionalized hexamolybdoaluminate / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBijelic, A. / Dobrov, A. / Roller, A. / Rompel, A.
Funding support1items
OrganizationGrant numberCountry
Austrian Science FundP27534
CitationJournal: Inorg.Chem. / Year: 2020
Title: Binding of a Fatty Acid-Functionalized Anderson-Type Polyoxometalate to Human Serum Albumin.
Authors: Bijelic, A. / Dobrov, A. / Roller, A. / Rompel, A.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4199
Polymers66,5711
Non-polymers3,8488
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint22 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.650, 38.540, 96.060
Angle α, β, γ (deg.)90.000, 105.110, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#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
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-M6O / lauric acid functionalized hexamolybdoaluminate


Mass: 1239.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30AlMo6NO25 / Feature type: SUBJECT OF INVESTIGATION
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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM potassium phosphate (pH 7.0), 150 mM KCl, 22-26% PEG3350, 125 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3→31.89 Å / Num. obs: 13029 / % possible obs: 96.13 % / Redundancy: 4.3 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 14.37
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1252 / CC1/2: 0.905 / CC star: 0.975

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5U

1n5u


Resolution: 3→31.89 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3112 --
Rwork0.2692 --
obs-13029 96.13 %
Displacement parametersBiso mean: 48.42 Å2
Refinement stepCycle: LAST / Resolution: 3→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 176 0 4679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164787
X-RAY DIFFRACTIONf_angle_d0.38886607
X-RAY DIFFRACTIONf_chiral_restr0.0318708
X-RAY DIFFRACTIONf_plane_restr0.003823
X-RAY DIFFRACTIONf_dihedral_angle_d17.0972941

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