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- PDB-3b9m: Human serum albumin complexed with myristate, 3'-azido-3'-deoxyth... -

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Basic information

Entry
Database: PDB / ID: 3b9m
TitleHuman serum albumin complexed with myristate, 3'-azido-3'-deoxythymidine (AZT) and salicylic acid
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / protein-ligands complex / Cleavage on pair of basic residues / Disease mutation / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Secreted
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
3'-azido-3'-deoxythymidine / MYRISTIC ACID / 2-HYDROXYBENZOIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhu, L. / Yang, F. / Chen, L. / Meehan, E.J. / Huang, M.
Citation
Journal: J.Struct.Biol. / Year: 2008
Title: A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography
Authors: Zhu, L. / Yang, F. / Chen, L. / Meehan, E.J. / Huang, M.
#1: Journal: 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.
#2: Journal: J.Struct.Biol. / Year: 2007
Title: Effect of human serum albumin on drug metabolism: structural evidence of esterase activity of human serum albumin
Authors: Yang, F. / Bian, C. / Zhu, L. / Zhao, G. / Huang, Z. / Huang, M.
#3: Journal: Nature / Year: 1992
Title: Atomic structure and chemistry of human serum albumin
Authors: He, X.M. / Carter, D.C.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2012Group: Non-polymer description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48510
Polymers66,5711
Non-polymers1,9149
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.536, 38.458, 95.368
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-AZZ / 3'-azido-3'-deoxythymidine / Azidothymidine / Zidovudine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32%(w/v) polyethylene glycol 3350, 50mM potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorDetector: CCD / Date: Aug 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→55 Å / Num. all: 15958 / Num. obs: 15958 / % possible obs: 54 % / Redundancy: 6 % / Biso Wilson estimate: 8 Å2
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 6 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7G

1e7g


Resolution: 2.7→46.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2355803 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1426 9 %RANDOM
Rwork0.242 ---
obs-15854 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.618 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å27.8 Å2
2--25.8 Å20 Å2
3----27.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 135 0 4765
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it8.081.5
X-RAY DIFFRACTIONc_mcangle_it12.612
X-RAY DIFFRACTIONc_scbond_it11.232
X-RAY DIFFRACTIONc_scangle_it16.042.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.47 148 9.3 %
Rwork0.41 1445 -
all-1593 -
obs--54.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2my.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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