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- PDB-8yg7: HSA Copper Indomethacin Complex -

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Basic information

Entry
Database: PDB / ID: 8yg7
TitleHSA Copper Indomethacin Complex
ComponentsAlbumin
KeywordsPROTEIN BINDING / Complex
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/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
: / INDOMETHACIN / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhang, Z.L. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077021 China
CitationJournal: To Be Published
Title: Human serum albumin-copper(II) agent-Indomethacin complex
Authors: Man, X.Y. / Yang, F.
History
DepositionFeb 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
I: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,84818
Polymers132,4302
Non-polymers4,41816
Water4,432246
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4249
Polymers66,2151
Non-polymers2,2098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4249
Polymers66,2151
Non-polymers2,2098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.347, 92.608, 95.219
Angle α, β, γ (deg.)75.02, 89.28, 79.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Albumin / HSA


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: Escherichia coli (E. coli) / References: UniProt: P02768
#2: Chemical ChemComp-A1D6U / ~{N},~{N}-dimethyl-7-propan-2-yl-3-thia-5-aza-1,6-diazonia-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(12),4,6,8,10-pentaen-4-amine


Mass: 312.901 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17CuN4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: evaporation
Details: PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, 4% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→91.93 Å / Num. obs: 68329 / % possible obs: 97.55 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.3
Reflection shellResolution: 2.09→2.1175 Å / Rmerge(I) obs: 0.0301 / Num. unique obs: 2644

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→91.93 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.85 / SU B: 10.032 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32452 3593 5 %RANDOM
Rwork0.26191 ---
obs0.26507 68174 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.09→91.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 288 246 9420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199382
X-RAY DIFFRACTIONr_bond_other_d0.0020.028586
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.99112692
X-RAY DIFFRACTIONr_angle_other_deg1.058319928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36951160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05624.596396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.737151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6861542
X-RAY DIFFRACTIONr_chiral_restr0.0920.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021828
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3693.3294646
X-RAY DIFFRACTIONr_mcbond_other2.3683.3284645
X-RAY DIFFRACTIONr_mcangle_it3.6284.9865804
X-RAY DIFFRACTIONr_mcangle_other3.6274.9865805
X-RAY DIFFRACTIONr_scbond_it2.8363.7084736
X-RAY DIFFRACTIONr_scbond_other2.8353.7094737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4865.4496889
X-RAY DIFFRACTIONr_long_range_B_refined7.37841.71611110
X-RAY DIFFRACTIONr_long_range_B_other7.36641.69411079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 8538 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.340.5
Imedium thermal3.242
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 248 -
Rwork0.335 5033 -
obs--96.25 %

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