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- PDB-6l4k: Human serum albumin-Palmitic acid-Cu compound -

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Basic information

Entry
Database: PDB / ID: 6l4k
TitleHuman serum albumin-Palmitic acid-Cu compound
ComponentsSerum albumin
KeywordsPROTEIN BINDING / Complex
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/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
Similarity search - Domain/homology
Chem-E5O / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhang, Z.L.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Novel Brain-Tumor-Inhibiting Copper(II) Compound Based on a Human Serum Albumin (HSA)-Cell Penetrating Peptide Conjugate.
Authors: Zhang, Z. / Yu, P. / Gou, Y. / Zhang, J. / Li, S. / Cai, M. / Sun, H. / Yang, F. / Liang, H.
History
DepositionOct 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: Serum albumin
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,90115
Polymers132,4302
Non-polymers3,47113
Water00
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1478
Polymers66,2151
Non-polymers1,9327
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint1 kcal/mol
Surface area28580 Å2
MethodPISA
2
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7537
Polymers66,2151
Non-polymers1,5396
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint2 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.356, 93.523, 96.359
Angle α, β, γ (deg.)74.890, 89.680, 80.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serum albumin


Mass: 66214.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Pichia kudriavzevii (yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-E5O / 2-bromanyl-9-ethyl-~{N},~{N},7-trimethyl-3-thia-1$l^{4},5,6$l^{4},10-tetraza-2$l^{4}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),4,6,9,11-pentaen-4-amine


Mass: 393.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16BrCuN5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: evaporation
Details: PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, and 4% DMSO.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→46.53 Å / Num. obs: 63319 / % possible obs: 97.91 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2
Reflection shellResolution: 2.09→2.139 Å / Rmerge(I) obs: 0.056 / Num. unique obs: 3977

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E7H

1e7h


Resolution: 2.09→46.53 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.052 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.304 / ESU R Free: 0.243
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 3379 5.1 %RANDOM
Rwork0.2358 ---
obs0.2385 63319 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.57 Å2 / Biso mean: 44.52 Å2 / Biso min: 23.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.15 Å20.01 Å2
2--0.25 Å20.04 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.09→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 220 0 9106
Biso mean--56.57 --
Num. residues----1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199307
X-RAY DIFFRACTIONr_bond_other_d0.0020.028539
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.98212580
X-RAY DIFFRACTIONr_angle_other_deg1.074319830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39851160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19324.596396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.046151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0981542
X-RAY DIFFRACTIONr_chiral_restr0.0960.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021814
LS refinement shellResolution: 2.09→2.139 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 213 -
Rwork0.347 3977 -
obs--98.1 %

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