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- PDB-2bx8: Human serum albumin complexed with azapropazone -

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Basic information

Entry
Database: PDB / ID: 2bx8
TitleHuman serum albumin complexed with azapropazone
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / LIPID-BINDING / FATTY ACID / METAL- BINDING / DRUG-BINDING / AZAPROPAZONE / TRANSPORT
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 / Heme degradation / Prednisone ADME / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Heme degradation / Prednisone ADME / 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
AZAPROPAZONE / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 25, 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 2.0May 30, 2018Group: Advisory / Data collection ...Advisory / Data collection / Non-polymer description / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / diffrn_source / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Dec 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 2.4Oct 23, 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)134,3446
Polymers133,1422
Non-polymers1,2014
Water00
1
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1723
Polymers66,5711
Non-polymers6012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1723
Polymers66,5711
Non-polymers6012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.200, 54.950, 119.903
Angle α, β, γ (deg.)81.21, 91.07, 64.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4369, 0.8991, 0.0258), (0.899, -0.4374, 0.0194), (0.0288, 0.0147, -0.9995)
Vector: -47.6072, -33.1096, 57.3403)

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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-AZQ / AZAPROPAZONE


Mass: 300.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20N4O2
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: 2.39 Å3/Da / Density % sol: 42 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.7→41.5 Å / Num. obs: 32332 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4

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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: 2.7→41.45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1038934.58 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: AZP AND AZQ IN THE TOPOLOGY THE DRUG AZAPROPAZONE BUT REFER TO THE DIFFERENT PUCKERS OF THE FUSED RING SYSTEM. AZQ.TOP AND AZQ.PAR WERE USED FOR A2001, WHILE AZP.TOP AND AZP.PAR WERE USED FOR A2002
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1528 4.7 %RANDOM
Rwork0.237 ---
obs0.237 32325 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.304 Å2 / ksol: 0.277814 e/Å3
Displacement parametersBiso mean: 77.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.67 Å2-10.04 Å28.36 Å2
2--3.29 Å2-7.8 Å2
3----10.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8581 0 88 0 8669
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
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: 2.7→2.87 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 235 4.4 %
Rwork0.354 5145 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AZQ.PARAZQ.TOP
X-RAY DIFFRACTION3AZP.PARAZP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAM

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