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- PDB-4la0: X-ray study of human serum albumin complexed with bicalutamide -

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Basic information

Entry
Database: PDB / ID: 4la0
TitleX-ray study of human serum albumin complexed with bicalutamide
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / PLASMA PROTEIN / CANCER / ONCOLOGY DRUG COMPLEX
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; 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
R-BICALUTAMIDE / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Z. / Ho, J.X. / Ruble, J. / Rose, J.P. / Carter, D.C.
Citation
Journal: Biochim.Biophys.Acta / Year: 2013
Title: Structural studies of several clinically important oncology drugs in complex with human serum albumin.
Authors: Wang, Z.M. / Ho, J.X. / Ruble, J.R. / Rose, J. / Ruker, F. / Ellenburg, M. / Murphy, R. / Click, J. / Soistman, E. / Wilkerson, L. / Carter, D.C.
#1: Journal: Burgers medicinal chemistry drug design and development, 7th edition
Year: 2010
Title: Crystallographic survey of albumin drug interaction and preliminary applications in cancer chemotherapy
Authors: Carter, D.C.
#2: Journal: Adv.Protein Chem. / Year: 1994
Title: Structure of Serum Albumin
Authors: Carter, D.C. / Ho, J.X.
#3: Journal: Eur.J.Biochem. / Year: 1994
Title: Preliminary crystallographic studies of four crystal forms of serum albumin.
Authors: Carter, D.C. / Chang, B. / Ho, J.X. / Keeling, K. / Krishnasami, Z.
#4: Journal: Nature / Year: 1993
Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin
Authors: Ho, X.M. / Carter, D.C.
#5: Journal: Nature / Year: 1992
Title: Atomic structure and chemistry of human serum albumin.
Authors: He, X.M. / Carter, D.C.
#6: Journal: Science / Year: 1990
Title: Structure of Human Serum Albumin
Authors: Carter, D.C. / Ho, X.M.
#7: Journal: Science / Year: 1989
Title: Three-dimensional structure of human serum albumin.
Authors: Carter, D.C. / He, X.M. / Munson, S.H. / Twigg, P.D. / Gernert, K.M. / Broom, M.B. / Miller, T.Y.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Other
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0034
Polymers133,1422
Non-polymers8612
Water3,297183
1
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0022
Polymers66,5711
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0022
Polymers66,5711
Non-polymers4301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.444, 59.568, 95.957
Angle α, β, γ (deg.)73.22, 83.93, 74.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain B and segid HSB)
NCS domain segments: (Selection details: chain 'B' and segid 'HSB ')

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Components

#1: Protein SERUM ALBUMIN


Mass: 66571.219 Da / Num. of mol.: 2 / Fragment: UNP residues 25-609 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-198 / R-BICALUTAMIDE / (2R)-N-[4-CYANO-3-(TRIFLUOROMETHYL)PHENYL]-3-[(4-FLUOROPHENYL)SULFONYL]-2-HYDROXY-2-METHYLPROPANAMIDE


Mass: 430.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14F4N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug ...Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug molar ratios, centered on the original crystallization hit using protocols described previously for the monoclinic [Carter, et al., Eur. J. Biochemistry (1994) 226: 1049-1052] and triclinic [Sugo, et al., Protein Eng (1999) 12: 439-446] crystal forms., pH 7.5, vapor diffusion, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: CONFOCAL OPTICS
RadiationMonochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 41969 / % possible obs: 93.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.41 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.490.45437940.674183.8
2.49-2.590.39140700.7190.4
2.59-2.70.29541180.783191.7
2.7-2.850.22941220.883192.4
2.85-3.020.1742321.028194.2
3.02-3.260.1242891.376195.6
3.26-3.580.0743411.575196.5
3.58-4.10.04743872.009197.2
4.1-5.160.03543712.143197.2
5.16-300.03342452.48194.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.861 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.98 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1877 4.47 %
Rwork0.1994 --
obs0.2018 41966 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.29 Å2 / Biso mean: 48.8271 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9241 0 58 183 9482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119517
X-RAY DIFFRACTIONf_angle_d1.44512803
X-RAY DIFFRACTIONf_chiral_restr0.1031413
X-RAY DIFFRACTIONf_plane_restr0.0071663
X-RAY DIFFRACTIONf_dihedral_angle_d15.8593607
Refine LS restraints NCSNumber: 5320 / Type: POSITIONAL / Rms dev position: 13.858 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.46490.36551270.28592706283382
2.4649-2.53740.29731410.26732955309690
2.5374-2.61930.34261340.24663002313691
2.6193-2.71280.3381440.24063068321292
2.7128-2.82140.29841440.2293060320492
2.8214-2.94970.27581460.23373086323294
2.9497-3.1050.29721490.22153121327095
3.105-3.29930.2751450.21193194333996
3.2993-3.55370.27731520.20333178333097
3.5537-3.91060.22511510.18233203335497
3.9106-4.47490.21831490.16743195334497
4.4749-5.63170.21691520.17833246339898
5.6317-29.86280.21881430.17853075321893

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