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- PDB-2bxk: Human serum albumin complexed with myristate, azapropazone and in... -

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Basic information

Entry
Database: PDB / ID: 2bxk
TitleHuman serum albumin complexed with myristate, azapropazone and indomethacin
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / LIPID-BINDING / METAL-BINDING / DRUG-BINDING / AZAPROPAZONE / MYRISTATE / INDOMETHACIN
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 / INDOMETHACIN / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2.0May 30, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Dec 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 2.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: SERUM ALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5729
Polymers66,5431
Non-polymers2,0288
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)188.100, 38.810, 95.530
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERUM ALBUMIN / HUMAN SERUM ALBUMIN


Mass: 66543.141 Da / Num. of mol.: 1
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-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication*YM
#4: Chemical ChemComp-AZQ / AZAPROPAZONE


Mass: 300.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE CONTAINS SIGNAL AND PRO-PEPTIDE (RESIDUES 1-24 IN DATABASE ENTRY). PROTEIN CRYSTALLISED ...SEQUENCE CONTAINS SIGNAL AND PRO-PEPTIDE (RESIDUES 1-24 IN DATABASE ENTRY). PROTEIN CRYSTALLISED WAS THE MATURE POLYPEPTIDE 25-609

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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: 2.53 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 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.4→22.3 Å / Num. obs: 25123 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7G

1e7g


Resolution: 2.4→21.56 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1792393.36 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1050 4.2 %RANDOM
Rwork0.209 ---
obs0.209 25121 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3534 Å2 / ksol: 0.335879 e/Å3
Displacement parametersBiso mean: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.52 Å20 Å23.24 Å2
2---1.66 Å20 Å2
3----8.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→21.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 137 24 4648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 72 1.7 %
Rwork0.276 4163 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2AZQ.PARAZQ.TOP
X-RAY DIFFRACTION3IMN.PARMYR.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMIMN.TOP
X-RAY DIFFRACTION5MYR.PAR

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