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- PDB-1h9z: Human Serum Albumin Complexed With Myristic Acid and the R-(+) en... -

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Basic information

Entry
Database: PDB / ID: 1h9z
TitleHuman Serum Albumin Complexed With Myristic Acid and the R-(+) enantiomer of warfarin
ComponentsSERUM ALBUMIN
KeywordsTRANSPORT PROTEIN / SERUM PROTEIN / DRUG BINDING / ANTI-COAGULANT
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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
MYRISTIC ACID / R-WARFARIN / Albumin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPetitpas, I. / Bhattacharya, A.A. / Curry, S.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure Analysis of Warfarin Binding to Human Serum Albumin: Anatomy of Drug Site I
Authors: Petitpas, I. / Bhattacharya, A.A. / Twine, S. / East, M. / Curry, S.
History
DepositionMar 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,2508
Polymers66,5711
Non-polymers1,6797
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.445, 38.842, 95.884
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERUM ALBUMIN / HSA


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / 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-RWF / R-WARFARIN


Mass: 308.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN HAS A 24 AA LEADER NOT PRESENT IN THE CRYSTAL

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Curry, S., (1998) Nat. Struct. Biol., 5, 827. / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mg/mlprotein1drop
225-30 %(w/v)PEG33501reservoir
350 mMpotassium phosphate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23090 / % possible obs: 98.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 4.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4
Reflection shell
*PLUS
% possible obs: 98.4 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7G

1e7g


Resolution: 2.5→29.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1680679.93 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1100 4.8 %RANDOM
Rwork0.204 ---
obs0.204 23090 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7223 Å2 / ksol: 0.282067 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.49 Å20 Å26.52 Å2
2---1.58 Å20 Å2
3----8.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 119 28 4734
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_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
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: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 184 4.9 %
Rwork0.304 3591 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MYR.PARMYR.TOP
X-RAY DIFFRACTION3WRR.OPEN.PARWRR.OPEN.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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