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- PDB-8zpa: Crystal structure of a HSA/probe complex -

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Basic information

Entry
Database: PDB / ID: 8zpa
TitleCrystal structure of a HSA/probe complex
ComponentsAlbumin
KeywordsSTRUCTURAL PROTEIN / Serum albumin
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / 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 / platelet alpha granule lumen / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / 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
PALMITIC ACID / STEARIC ACID / : / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYoun, S.Y. / Cha, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomaterials / Year: 2025
Title: Conversion of albumin into a BODIPY-like photosensitizer by a flick reaction, tumor accumulation and photodynamic therapy.
Authors: Yang, M. / Kim, Y. / Youn, S.Y. / Jeong, H. / Shirbhate, M.E. / Uhm, C. / Kim, G. / Nam, K.T. / Cha, S.S. / Kim, K.M. / Yoon, J.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3087
Polymers67,3461
Non-polymers9626
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: We observed an increase in fluorescence intensity upon the formation of a complex between the protein and the chemical
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.705, 38.441, 93.290
Angle α, β, γ (deg.)90.000, 103.920, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Albumin / HSA


Mass: 67346.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-UI8 / 7-$l^{3}-oxidanyl-12~{H}-[2,1]benzazaborolo[2,1-a][1,3,2]benzodiazaborinine


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12BN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 315 K / Method: microbatch / pH: 7.5
Details: 30% polyethylene glycol monomethyl ether 550, 0.1 M HEPES pH 7.5, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.491→50 Å / Num. obs: 21415 / % possible obs: 99.5 % / Redundancy: 6.78 % / Biso Wilson estimate: 69.47 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 2.55→2.65 Å / Num. unique obs: 2078 / CC1/2: 0.675

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→37.04 Å / SU ML: 0.4221 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 29.4891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 1936 10 %
Rwork0.2372 17420 -
obs0.2401 19356 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.29 Å2
Refinement stepCycle: LAST / Resolution: 2.59→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 68 0 4408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254493
X-RAY DIFFRACTIONf_angle_d0.50156085
X-RAY DIFFRACTIONf_chiral_restr0.0333689
X-RAY DIFFRACTIONf_plane_restr0.0034793
X-RAY DIFFRACTIONf_dihedral_angle_d15.25751621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.59-2.680.37160.3192X-RAY DIFFRACTION79
2.68-2.790.35330.2928X-RAY DIFFRACTION89
2.79-2.910.31251290.274X-RAY DIFFRACTION95
2.91-3.070.3151350.2952X-RAY DIFFRACTION95
3.07-3.260.33710.2842X-RAY DIFFRACTION98
3.26-3.510.31950.2706X-RAY DIFFRACTION98
3.51-3.860.28540.2453X-RAY DIFFRACTION98
3.86-4.420.24950.214X-RAY DIFFRACTION97
4.42-5.570.23890.2147X-RAY DIFFRACTION96

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