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- PDB-9hnb: X-ray structure of the adduct formed upon reaction of the diiodid... -

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Basic information

Entry
Database: PDB / ID: 9hnb
TitleX-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with human serum albumin
ComponentsSerum albumin
KeywordsHYDROLASE / platin / interaction / metallodrug / picoplatin / diiodido analogue / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsFerraro, G. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)2022JMFC3X Italy
CitationJournal: Inorg.Chem. / Year: 2025
Title: Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin.
Authors: Ferraro, G. / Pracharova, J. / Gotte, G. / Massai, L. / Berecka, M. / Starha, P. / Messori, L. / Merlino, A.
History
DepositionDec 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1564
Polymers66,5711
Non-polymers5853
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-52 kcal/mol
Surface area26280 Å2
Unit cell
Length a, b, c (Å)58.070, 86.550, 59.500
Angle α, β, γ (deg.)90.000, 102.548, 90.000
Int Tables number4
Space group name H-MP1211

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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-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% PEG3350 -50 mM potassium phosphate buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→47.42 Å / Num. obs: 5252 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.3
Reflection shellResolution: 3.9→3.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 260 / CC1/2: 0.568 / Rpim(I) all: 0.573 / Rrim(I) all: 1.097 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→47.42 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.83 / SU B: 89.719 / SU ML: 1.224 / Cross valid method: FREE R-VALUE / ESU R Free: 1.257
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3275 263 5.296 %
Rwork0.2917 4703 -
all0.293 --
obs-4966 93.363 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 112.871 Å2
Baniso -1Baniso -2Baniso -3
1--1.282 Å2-0 Å21.783 Å2
2---0.81 Å2-0 Å2
3---1.181 Å2
Refinement stepCycle: LAST / Resolution: 3.9→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 3 0 4198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173906
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0040.018189
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6485827
X-RAY DIFFRACTIONr_angle_other_deg1.5971.5769074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92323.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18915727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7431520
X-RAY DIFFRACTIONr_chiral_restr0.10.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
X-RAY DIFFRACTIONr_nbd_refined0.2750.21209
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23718
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22153
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.212
X-RAY DIFFRACTIONr_nbd_other0.2280.217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4450.21
X-RAY DIFFRACTIONr_mcbond_it5.75712.2792169
X-RAY DIFFRACTIONr_mcbond_other5.73312.2742168
X-RAY DIFFRACTIONr_mcangle_it9.83918.412706
X-RAY DIFFRACTIONr_mcangle_other9.84218.4152707
X-RAY DIFFRACTIONr_scbond_it5.21812.6612125
X-RAY DIFFRACTIONr_scbond_other5.21812.6552123
X-RAY DIFFRACTIONr_scangle_it9.17518.8243121
X-RAY DIFFRACTIONr_scangle_other9.17418.8243121
X-RAY DIFFRACTIONr_lrange_it17.921254.1210469
X-RAY DIFFRACTIONr_lrange_other17.918254.10610469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.0010.396220.317274X-RAY DIFFRACTION77.6903
4.001-4.110.418130.301280X-RAY DIFFRACTION80.274
4.11-4.2280.422130.287305X-RAY DIFFRACTION84.5745
4.228-4.3580.272190.281308X-RAY DIFFRACTION87.4332
4.358-4.50.406150.246294X-RAY DIFFRACTION91.9643
4.5-4.6570.399150.258298X-RAY DIFFRACTION93.7126
4.657-4.8310.31220.232314X-RAY DIFFRACTION99.7033
4.831-5.0270.268250.264279X-RAY DIFFRACTION99.0228
5.027-5.2490.249170.23288X-RAY DIFFRACTION100
5.249-5.5030.41460.278279X-RAY DIFFRACTION100
5.503-5.7980.325150.314261X-RAY DIFFRACTION98.9247
5.798-6.1460.447190.32230X-RAY DIFFRACTION97.6471
6.146-6.5650.348100.315240X-RAY DIFFRACTION99.2063
6.565-7.0830.336120.301208X-RAY DIFFRACTION99.0991
7.083-7.7480.376100.271194X-RAY DIFFRACTION99.0291
7.748-8.6430.284110.265187X-RAY DIFFRACTION99
8.643-9.9430.28680.268152X-RAY DIFFRACTION95.8084
9.943-12.090.06740.3142X-RAY DIFFRACTION97.9866
12.09-16.7390.39950.379105X-RAY DIFFRACTION97.3451

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