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- PDB-5ifo: X-ray structure of HSA-Myr-KP1019 -

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Basic information

Entry
Database: PDB / ID: 5ifo
TitleX-ray structure of HSA-Myr-KP1019
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Complex / anticancer drug / serum protein
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule 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; 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
MYRISTIC ACID / RUTHENIUM ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBijelic, A. / Theiner, S. / Keppler, B.K. / Rompel, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP23711 Austria
CitationJournal: J.Med.Chem. / Year: 2016
Title: X-ray Structure Analysis of Indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) Bound to Human Serum Albumin Reveals Two Ruthenium Binding Sites and Provides Insights into ...Title: X-ray Structure Analysis of Indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) Bound to Human Serum Albumin Reveals Two Ruthenium Binding Sites and Provides Insights into the Drug Binding Mechanism.
Authors: Bijelic, A. / Theiner, S. / Keppler, B.K. / Rompel, A.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)68,1449
Polymers66,5711
Non-polymers1,5728
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint33 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.110, 38.060, 94.950
Angle α, β, γ (deg.)90.00, 105.06, 90.00
Int Tables number5
Space group name H-MC121

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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-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 75-120 mg/ml protein, 50 mM potassium phosphate, 25-30% PEG4000, 150 mM KCl, 5 mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 3.2→45.844 Å / Num. obs: 10508 / % possible obs: 98 % / Redundancy: 3.4 % / Net I/σ(I): 17.89

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata scaling
PHENIX(1.10_2155)phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9M

3b9m


Resolution: 3.2→45.844 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 30.21
Details: During processing the data was cut at 2.93 A due to suitable values for I/sigma, CC1/2 etc. However, during refinement a great drop in data completeness beginning at >3.2 A was recognized ...Details: During processing the data was cut at 2.93 A due to suitable values for I/sigma, CC1/2 etc. However, during refinement a great drop in data completeness beginning at >3.2 A was recognized and in addition the FOM was too small and the expected R-values were ridicilously high. The result was a blurry and strange looking map. Therefore, a 3.2 A cutoff was set during refinement.
RfactorNum. reflection% reflection
Rfree0.2615 959 4.95 %
Rwork0.2441 --
obs0.245 10501 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4583 0 90 9 4682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164783
X-RAY DIFFRACTIONf_angle_d0.4136427
X-RAY DIFFRACTIONf_dihedral_angle_d10.6373007
X-RAY DIFFRACTIONf_chiral_restr0.034707
X-RAY DIFFRACTIONf_plane_restr0.003827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.36870.37831330.36182619X-RAY DIFFRACTION96
3.3687-3.57970.34231300.34482549X-RAY DIFFRACTION93
3.5797-3.85590.35631360.29672632X-RAY DIFFRACTION96
3.8559-4.24370.2551430.25662667X-RAY DIFFRACTION97
4.2437-4.85720.21671370.21972692X-RAY DIFFRACTION98
4.8572-6.11720.29211360.23622590X-RAY DIFFRACTION96
6.1172-45.84830.19191440.17642648X-RAY DIFFRACTION97

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