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- PDB-7d6j: Human serum albumin complexed with benzbromarone -

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Basic information

Entry
Database: PDB / ID: 7d6j
TitleHuman serum albumin complexed with benzbromarone
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / human serum albumin / drug complex
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsKawai, A. / Yamasaki, K.
CitationJournal: Mol Pharm. / Year: 2021
Title: Interaction of Benzbromarone with Subdomains IIIA and IB/IIA on Human Serum Albumin as the Primary and Secondary Binding Regions.
Authors: Yamasaki, K. / Kawai, A. / Sakurama, K. / Udo, N. / Yoshino, Y. / Saito, Y. / Tsukigawa, K. / Nishi, K. / Otagiri, M.
History
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,53510
Polymers133,1422
Non-polymers3,3938
Water00
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2685
Polymers66,5711
Non-polymers1,6964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2685
Polymers66,5711
Non-polymers1,6964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.372, 179.727, 59.658
Angle α, β, γ (deg.)90.000, 105.231, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#2: Chemical
ChemComp-R75 / [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-1-benzofuran-3-yl)methanone / Benzbromarone


Mass: 424.083 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H12Br2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiarrhythmic, inhibitor*YM
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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 34% PEG 3350, 50mM K phosphate buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 17867 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 120.71 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.97
Reflection shellResolution: 3.29→3.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2849 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YOQ

5yoq


Resolution: 3.29→48.47 Å / SU ML: 0.5928 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 39.3232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3205 894 5.01 %
Rwork0.2712 16962 -
obs0.2738 17856 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.87 Å2
Refinement stepCycle: LAST / Resolution: 3.29→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 176 0 7464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00157614
X-RAY DIFFRACTIONf_angle_d0.403110488
X-RAY DIFFRACTIONf_chiral_restr0.03541235
X-RAY DIFFRACTIONf_plane_restr0.00361417
X-RAY DIFFRACTIONf_dihedral_angle_d9.57472432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.50.40881480.35892806X-RAY DIFFRACTION99.06
3.5-3.770.38181480.3342817X-RAY DIFFRACTION99.63
3.77-4.150.34741490.30272818X-RAY DIFFRACTION99.76
4.15-4.750.33071480.28252825X-RAY DIFFRACTION99.6
4.75-5.980.34841510.30932855X-RAY DIFFRACTION99.77
5.98-48.470.27281500.21742841X-RAY DIFFRACTION99.3

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