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- PDB-4s1y: X-ray structure of human serum albumin complexed with cisplatin -

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Basic information

Entry
Database: PDB / ID: 4s1y
TitleX-ray structure of human serum albumin complexed with cisplatin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Albumin / drug transport / fatty acids
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; 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsMerlino, A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: Cisplatin binding to human serum albumin: a structural study.
Authors: Ferraro, G. / Massai, L. / Messori, L. / Merlino, A.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_site
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0716
Polymers66,5711
Non-polymers1,5005
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.789, 86.474, 59.141
Angle α, β, γ (deg.)90.00, 103.70, 90.00
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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
References: UniProt: P02768
#2: Chemical
ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a ...Details: Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a reservoir solution of 30 % w/v polyethylene glycol 3350 in 50 mM potassium phosphate at pH 7.4 and protein concentration of 30 mg mL-1 (see experimental section or further details), were soaked for 24 h in a 0.005 M cisplatin solution in the same reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.16→57.46 Å / Num. all: 9393 / Num. obs: 9393 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.149

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1HK1

1hk1


Resolution: 3.16→57.46 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.759 / SU B: 36.56 / SU ML: 0.616 / Cross valid method: THROUGHOUT / ESU R Free: 0.737 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32943 449 4.8 %RANDOM
Rwork0.22311 ---
all0.22781 ---
obs0.22781 8934 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.033 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å2-0 Å20.72 Å2
2---0.98 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 3.16→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 11 11 4217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194305
X-RAY DIFFRACTIONr_bond_other_d0.0030.024008
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9745839
X-RAY DIFFRACTIONr_angle_other_deg0.82939243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94724.737190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5711520
X-RAY DIFFRACTIONr_chiral_restr0.070.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.844.9292169
X-RAY DIFFRACTIONr_mcbond_other2.8334.9282168
X-RAY DIFFRACTIONr_mcangle_it4.7337.3892706
X-RAY DIFFRACTIONr_mcangle_other4.7337.392707
X-RAY DIFFRACTIONr_scbond_it2.815.1472136
X-RAY DIFFRACTIONr_scbond_other2.815.1482137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6397.623134
X-RAY DIFFRACTIONr_long_range_B_refined7.72239.3725430
X-RAY DIFFRACTIONr_long_range_B_other7.72239.3755431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.163→3.245 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 35 -
Rwork0.325 615 -
obs--92.59 %

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