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- PDB-6qs9: Bovine Serum Albumin in complex with Ketoprofen -

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Basic information

Entry
Database: PDB / ID: 6qs9
TitleBovine Serum Albumin in complex with Ketoprofen
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Non-steroidal anti-inflammatory drug / plasma protein
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex / DNA binding / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(R)-Ketoprofen / Albumin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsDonini, S. / Parisini, E.
CitationJournal: Acs Omega / Year: 2019
Title: Biohybrid Electrospun Membrane for the Filtration of Ketoprofen Drug from Water.
Authors: Castagna, R. / Donini, S. / Colnago, P. / Serafini, A. / Parisini, E. / Bertarelli, C.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4628
Polymers138,7932
Non-polymers6696
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-31 kcal/mol
Surface area54720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.486, 44.374, 142.715
Angle α, β, γ (deg.)90.00, 113.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin / BSA


Mass: 69396.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ALB / Production host: Bos taurus (cattle) / References: UniProt: P02769
#2: Chemical ChemComp-JGE / (R)-Ketoprofen


Mass: 254.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% MMEPEG 5000, 0.2M ammonium chloride, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.59 Å / Num. obs: 30574 / % possible obs: 99.5 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.2
Reflection shellResolution: 2.8→2.89 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OR0

4or0


Resolution: 2.802→46.585 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2723 1526 4.99 %
Rwork0.2152 --
obs0.2181 30559 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→46.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9226 0 42 77 9345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119490
X-RAY DIFFRACTIONf_angle_d1.32912764
X-RAY DIFFRACTIONf_dihedral_angle_d16.3063598
X-RAY DIFFRACTIONf_chiral_restr0.0551414
X-RAY DIFFRACTIONf_plane_restr0.0081656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8023-2.89280.43021470.36562549X-RAY DIFFRACTION99
2.8928-2.99610.39491520.30172642X-RAY DIFFRACTION100
2.9961-3.11610.37261560.27552585X-RAY DIFFRACTION100
3.1161-3.25790.34941370.26142616X-RAY DIFFRACTION100
3.2579-3.42960.33411240.25882673X-RAY DIFFRACTION100
3.4296-3.64440.28551520.22822620X-RAY DIFFRACTION100
3.6444-3.92560.28131370.2052615X-RAY DIFFRACTION100
3.9256-4.32040.27271380.19422647X-RAY DIFFRACTION99
4.3204-4.9450.25881200.19232684X-RAY DIFFRACTION99
4.945-6.22780.27521160.22852667X-RAY DIFFRACTION98
6.2278-46.59160.20721470.18382735X-RAY DIFFRACTION98

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