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- PDB-3uiv: Human serum albumin-myristate-amantadine hydrochloride complex -

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Basic information

Entry
Database: PDB / ID: 3uiv
TitleHuman serum albumin-myristate-amantadine hydrochloride complex
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / fatty acid / plasma
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / 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
(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, F. / Ma, Z. / Ma, L. / Yang, G.
CitationJournal: TO BE PUBLISHED
Title: Structural basis of the drug-binding specificity of human serum albumin
Authors: Curry, S.
History
DepositionNov 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 30, 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
H: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,26316
Polymers133,1422
Non-polymers3,12014
Water8,791488
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9417
Polymers66,5711
Non-polymers1,3706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
H: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3219
Polymers66,5711
Non-polymers1,7508
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.270, 93.516, 96.217
Angle α, β, γ (deg.)74.91, 89.75, 80.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2 / 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.: 13 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-308 / (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine / Amantadine


Mass: 151.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32% (w/v) polyethylene glycol 3350, 50mM potassium phosphate (pH 7.5), 5% glycerol, 3% DMSO, 2% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jun 28, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 66700 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 13.4
Reflection shellHighest resolution: 2.1 Å / % possible all: 95

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6_289refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ5

1bj5


Resolution: 2.2→37.389 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7597 / SU ML: 0.38 / σ(F): 1.97 / Phase error: 31.33 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2902 3151 5.08 %
Rwork0.2262 --
obs0.2295 61999 96.35 %
all-60000 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.262 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 127.52 Å2 / Biso mean: 42.9789 Å2 / Biso min: 15.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.2982 Å2-0.1283 Å2-0.176 Å2
2---0.4797 Å2-0.1547 Å2
3---0.1814 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8942 0 203 488 9633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089346
X-RAY DIFFRACTIONf_angle_d1.12612559
X-RAY DIFFRACTIONf_dihedral_angle_d17.9473448
X-RAY DIFFRACTIONf_chiral_restr0.0751416
X-RAY DIFFRACTIONf_plane_restr0.0051622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27860.35973110.28895917622897
2.2786-2.36980.30243120.25345947625997
2.3698-2.47770.3242970.24265914621197
2.4777-2.60830.32463100.24835965627597
2.6083-2.77160.35063140.24695987630197
2.7716-2.98560.30683260.24195969629598
2.9856-3.28580.30743300.22785893622397
3.2858-3.76090.29323170.21575849616696
3.7609-4.73690.23713070.18785572587991
4.7369-37.3940.26433270.21715835616296
Refinement TLS params.Method: refined / Origin x: 8.7171 Å / Origin y: 20.2286 Å / Origin z: 19.1059 Å
111213212223313233
T0.1292 Å20.0181 Å20.0149 Å2-0.185 Å2-0.0072 Å2--0.1881 Å2
L0.0334 °20.0846 °20.0335 °2-0.2664 °20.0467 °2--0.2923 °2
S-0.0142 Å °0.0175 Å °0.0028 Å °-0.0146 Å °0.0076 Å °-0.0147 Å °0.0118 Å °0.0065 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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