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- PDB-3lu7: Human serum albumin in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 3lu7
TitleHuman serum albumin in complex with compound 2
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Binding Sites / Ligands / Protein Binding / Serum Albumin / HSA / PROTEROS BIOSTRUCTURES GMBH / ASTRAZENECA / Drug Design
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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; 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
Chem-IPX / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsButtar, D. / Colclough, N. / Gerhardt, S. / MacFaul, P.A. / Phillips, S.D. / Plowright, A. / Whittamore, P. / Tam, K. / Maskos, K. / Steinbacher, S. / Steuber, H.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: A combined spectroscopic and crystallographic approach to probing drug-human serum albumin interactions
Authors: Buttar, D. / Colclough, N. / Gerhardt, S. / Macfaul, P.A. / Phillips, S.D. / Plowright, A. / Whittamore, P. / Tam, K. / Maskos, K. / Steinbacher, S. / Steuber, H.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3789
Polymers133,1422
Non-polymers1,2367
Water543
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2375
Polymers66,5711
Non-polymers6654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1424
Polymers66,5711
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.541, 59.185, 95.603
Angle α, β, γ (deg.)75.30, 87.86, 75.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-IPX / 4-[(1R,2R)-2-{[(5-fluoro-1H-indol-2-yl)carbonyl]amino}-2,3-dihydro-1H-inden-1-yl]butanoic acid


Mass: 380.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21FN2O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.38 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 9, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.8→92.45 Å / Num. all: 29572 / Num. obs: 29572 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.2 / % possible all: 90.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.2.0005refinement
SCALAdata scaling
RefinementResolution: 2.8→55.44 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 17.738 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27583 1392 5.1 %RANDOM
Rwork0.2252 ---
all0.23574 26029 --
obs0.22771 26029 92.73 %-
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 mean: 66.006 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å2-3.22 Å2-1.32 Å2
2--1.77 Å21.59 Å2
3----3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→55.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 81 3 9291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229492
X-RAY DIFFRACTIONr_bond_other_d0.0010.028410
X-RAY DIFFRACTIONr_angle_refined_deg1.121.98112834
X-RAY DIFFRACTIONr_angle_other_deg0.76319754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67751154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41824.933446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.941151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9741548
X-RAY DIFFRACTIONr_chiral_restr0.0580.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021838
X-RAY DIFFRACTIONr_nbd_refined0.2260.22443
X-RAY DIFFRACTIONr_nbd_other0.1620.28417
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24527
X-RAY DIFFRACTIONr_nbtor_other0.0840.25315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.78327541
X-RAY DIFFRACTIONr_mcbond_other0.30322290
X-RAY DIFFRACTIONr_mcangle_it2.32439352
X-RAY DIFFRACTIONr_scbond_it3.43644310
X-RAY DIFFRACTIONr_scangle_it4.99263482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 106 -
Rwork0.348 1794 -
obs--87.44 %

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