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- PDB-2i2z: Human serum albumin complexed with myristate and aspirin -

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Basic information

Entry
Database: PDB / ID: 2i2z
TitleHuman serum albumin complexed with myristate and aspirin
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / PLASMA PROTEIN / METAL-BINDING / LIPID-BINDING
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule 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
MYRISTIC ACID / 2-HYDROXYBENZOIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYang, F. / Bian, C. / Zhu, L. / Zhao, G. / Huang, Z. / Huang, M.
CitationJournal: 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.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)67,8927
Polymers66,6121
Non-polymers1,2806
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.409, 38.936, 96.018
Angle α, β, γ (deg.)90.00, 105.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin


Mass: 66612.250 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.: 5 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: evaporation, vapor diffusion, sitting drop / pH: 7.5
Details: 31-34% (w/v) PEG 3350, 50mM potassium phosphate (pH 7.5). Crystals grew spontaneously as clusters of rods after three days. Technique of streak-seeding was used to improve crystal quality., ...Details: 31-34% (w/v) PEG 3350, 50mM potassium phosphate (pH 7.5). Crystals grew spontaneously as clusters of rods after three days. Technique of streak-seeding was used to improve crystal quality., EVAPORATION, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 2000 / Detector: CCD / Date: Aug 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→57.81 Å / Num. all: 19112 / Num. obs: 17851 / % possible obs: 93.4 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 9.34 / Biso Wilson estimate: 41.5 Å2
Reflection shellResolution: 2.7→2.87 Å / % possible all: 89.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ5

1bj5


Resolution: 2.7→57.68 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1715489.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 709 3.8 %RANDOM
Rwork0.218 ---
obs0.218 16893 98 %-
all-19112 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3416 Å2 / ksol: 0.310277 e/Å3
Displacement parametersBiso mean: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.01 Å20 Å27.48 Å2
2--1.78 Å20 Å2
3----11.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→57.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 90 0 4723
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.381.5
X-RAY DIFFRACTIONc_mcangle_it9.92
X-RAY DIFFRACTIONc_scbond_it11.472
X-RAY DIFFRACTIONc_scangle_it16.472.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 75 2.4 %
Rwork0.335 3035 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hsa_par.txt
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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