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- PDB-7wok: Crystal structure of HSA soaked with cisplatin for one week -

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Basic information

Entry
Database: PDB / ID: 7wok
TitleCrystal structure of HSA soaked with cisplatin for one week
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Human serum albumin / Cisplatin
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
Cisplatin / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, S.L. / Yuan, C. / Jiang, L.G. / Luo, Z.P. / Huang, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystallographic analysis of interaction between cisplatin and human serum albumin: Effect of fatty acid.
Authors: Chen, S.L. / Yuan, C. / Jiang, L.G. / Luo, Z.P. / Huang, M.D.
History
DepositionJan 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,13014
Polymers138,9392
Non-polymers3,19012
Water30617
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0657
Polymers69,4701
Non-polymers1,5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0657
Polymers69,4701
Non-polymers1,5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.376, 180.518, 58.503
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Albumin


Mass: 69469.695 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-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 26-32% PEG 3350, 50mM PB at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.873
11-L, -K, -H20.127
ReflectionResolution: 2.9→50 Å / Num. obs: 25610 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2520 / CC1/2: 0.667 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.9→36.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.299 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1287 5 %RANDOM
Rwork0.2066 ---
obs0.2084 24293 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 396.71 Å2 / Biso mean: 116.83 Å2 / Biso min: 42.93 Å2
Baniso -1Baniso -2Baniso -3
1-38.67 Å20 Å259.58 Å2
2--4.78 Å20 Å2
3----43.45 Å2
Refinement stepCycle: final / Resolution: 2.9→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8924 0 40 17 8981
Biso mean--111.63 79.56 -
Num. residues----1119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139174
X-RAY DIFFRACTIONr_bond_other_d0.0030.0158674
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.6512369
X-RAY DIFFRACTIONr_angle_other_deg0.5521.59320121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2274.961124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14323.486479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.275151689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4631546
X-RAY DIFFRACTIONr_chiral_restr0.0630.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0480.0210176
X-RAY DIFFRACTIONr_gen_planes_other0.0420.021963
X-RAY DIFFRACTIONr_mcbond_it28.31323.9944471
X-RAY DIFFRACTIONr_mcbond_other28.30223.9944470
X-RAY DIFFRACTIONr_mcangle_it32.65344.9865582
LS refinement shellResolution: 2.905→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 97 -
Rwork0.242 1577 -
all-1674 -
obs--89.52 %

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