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- PDB-7woj: Crystal structure of HSA-Myr complex soaked with cisplatin for on... -

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Basic information

Entry
Database: PDB / ID: 7woj
TitleCrystal structure of HSA-Myr complex soaked with cisplatin for one week
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Human serum albumin / Fatty acid / Cisplatin
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 / fatty acid binding / cellular response to starvation / 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 / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / 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 / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)73,54016
Polymers69,4701
Non-polymers4,07115
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.910, 36.690, 90.010
Angle α, β, γ (deg.)90.000, 105.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Albumin


Mass: 69469.695 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
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Chemical
ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / 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: 0.932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 12296 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.156 / Net I/σ(I): 14.8
Reflection shellResolution: 2.89→3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 4.652 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1202 / CC1/2: 0.254 / % 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: 3TDL

3tdl


Resolution: 2.89→43.41 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.903 / SU B: 21.732 / SU ML: 0.427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.581 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 562 5.2 %RANDOM
Rwork0.2575 ---
obs0.2589 10194 86.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 235.21 Å2 / Biso mean: 87.872 Å2 / Biso min: 36.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å2-0 Å20.65 Å2
2---1.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.89→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 118 0 4478
Biso mean--96.82 --
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134572
X-RAY DIFFRACTIONr_bond_other_d0.0090.0154315
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.6556128
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5959966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49623.229223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89615763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8041522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025068
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02982
X-RAY DIFFRACTIONr_mcbond_it12.079.2252259
X-RAY DIFFRACTIONr_mcbond_other12.0699.2242257
X-RAY DIFFRACTIONr_mcangle_it17.74413.8372813
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 5 -
Rwork0.255 240 -
all-245 -
obs--27.37 %

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