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- PDB-2bxb: Human serum albumin complexed with oxyphenbutazone -

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Basic information

Entry
Database: PDB / ID: 2bxb
TitleHuman serum albumin complexed with oxyphenbutazone
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / LIPID-BINDING / METAL-BINDING / DRUG-BINDING / OXYPHENBUTAZONE
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGhuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Curry, S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Basis of the Drug-Binding Specificity of Human Serum Albumin.
Authors: Ghuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Otagiri, M. / Curry, S.
History
DepositionJul 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 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: SERUM ALBUMIN
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7914
Polymers133,1422
Non-polymers6492
Water00
1
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8962
Polymers66,5711
Non-polymers3241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8962
Polymers66,5711
Non-polymers3241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.160, 55.500, 120.510
Angle α, β, γ (deg.)81.33, 90.52, 65.38
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4262, 0.9043, 0.0252), (0.9044, -0.4266, 0.0099), (0.0197, 0.0186, -0.9996)
Vector: -47.9085, -33.9479, 58.1838)

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Components

#1: Protein SERUM ALBUMIN / HUMAN SERUM ALBUMIN


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-OPB / 4-BUTYL-1-(4-HYDROXYPHENYL)-2-PHENYLPYRAZOLIDINE-3,5-DIONE / OXYPHENBUTAZONE


Mass: 324.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N2O3 / Comment: antiinflammatory*YM
Has protein modificationY
Sequence detailsSEQUENCE IS FOR PRE-CURSOR. MATURE POLYPEPTIDE WAS CRYSTALLISED (WHICH LACKS SIGNAL AND PROPEPTIDES ...SEQUENCE IS FOR PRE-CURSOR. MATURE POLYPEPTIDE WAS CRYSTALLISED (WHICH LACKS SIGNAL AND PROPEPTIDES - RESIDUES 1-24)

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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: 2.48 Å3/Da / Density % sol: 44 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.2→22.9 Å / Num. obs: 22484 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E78

1e78


Resolution: 3.2→22.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 857866.59 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 992 4.8 %RANDOM
Rwork0.228 ---
obs0.228 20632 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.686 Å2 / ksol: 0.212583 e/Å3
Displacement parametersBiso mean: 71 Å2
Baniso -1Baniso -2Baniso -3
1-10.31 Å2-12.02 Å25.4 Å2
2--2.6 Å2-3.97 Å2
3----12.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.2→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8742 0 48 0 8790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 175 5.1 %
Rwork0.277 3259 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2OXY.SC-OPP.PAROXY.SC-OPP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM

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