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- PDB-5gix: Human serum albumin-Palmitic acid-Fe(Hn3piT)Cl2 -

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Basic information

Entry
Database: PDB / ID: 5gix
TitleHuman serum albumin-Palmitic acid-Fe(Hn3piT)Cl2
ComponentsSerum albumin
KeywordsIMMUNE SYSTEM / ferric compound / anticancer mechanism / tumor targeting / therapeutic effect
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
Chem-6WF / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsYang, F. / Qi, J. / Wang, T.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Developing Anticancer Ferric Prodrugs Based on the N-Donor Residues of Human Serum Albumin Carrier IIA Subdomain
Authors: Qi, J. / Gou, Y. / Zhang, Y. / Yang, K. / Chen, S. / Liu, L. / Wu, X. / Wang, T. / Zhang, W. / Yang, F.
History
DepositionJun 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,24316
Polymers132,4302
Non-polymers3,81414
Water362
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1228
Polymers66,2151
Non-polymers1,9077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint8 kcal/mol
Surface area29330 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1228
Polymers66,2151
Non-polymers1,9077
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint7 kcal/mol
Surface area29320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.472, 94.550, 96.105
Angle α, β, γ (deg.)104.90, 89.90, 100.86
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 / Fragment: UNP residues 27-607
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-6WF / 14-piperidin-1-yl-11-oxa-13$l^{3}-thia-15,16$l^{4}-diaza-12$l^{3}-ferratetracyclo[8.7.0.0^{2,7}.0^{12,16}]heptadeca-1(10),2(7),3,5,8,13,16-heptaene


Mass: 368.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18FeN3OS
#3: Chemical
ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4
Details: PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, and 4% DMSO.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→28 Å / Num. obs: 30492 / % possible obs: 96 % / Redundancy: 4.2 % / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bj5

1bj5


Resolution: 2.801→27.126 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1994 6.54 %
Rwork0.2094 --
obs0.2133 30492 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→27.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9212 0 248 2 9462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029677
X-RAY DIFFRACTIONf_angle_d0.66812946
X-RAY DIFFRACTIONf_dihedral_angle_d16.1543718
X-RAY DIFFRACTIONf_chiral_restr0.0241418
X-RAY DIFFRACTIONf_plane_restr0.0031666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8008-2.87080.4091390.30551958X-RAY DIFFRACTION93
2.8708-2.94830.281420.27152056X-RAY DIFFRACTION96
2.9483-3.0350.33211330.26272000X-RAY DIFFRACTION98
3.035-3.13280.34851450.26752082X-RAY DIFFRACTION98
3.1328-3.24460.30871470.26672052X-RAY DIFFRACTION96
3.2446-3.37430.28811420.25042046X-RAY DIFFRACTION99
3.3743-3.52750.31511450.24312071X-RAY DIFFRACTION97
3.5275-3.71310.28011470.22252061X-RAY DIFFRACTION99
3.7131-3.9450.30191490.2132066X-RAY DIFFRACTION98
3.945-4.24860.24441410.18842067X-RAY DIFFRACTION97
4.2486-4.67420.23791380.18062036X-RAY DIFFRACTION97
4.6742-5.3460.21881420.18152054X-RAY DIFFRACTION97
5.346-6.71850.25171430.20872063X-RAY DIFFRACTION98
6.7185-27.12690.22271410.15531886X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.02590.19380.03251.27670.15270.64050.0247-0.00160.0435-0.010.029-0.0179-0.0758-0.0928-0.05040.20350.12410.04440.2818-0.0090.42010.13820.2589-1.2401
2-0.24920.0809-0.36051.02450.04171.074-0.0539-0.0368-0.0302-0.00720.1012-0.01240.3068-0.15240.01090.3706-0.0408-0.04440.51860.01230.462619.3625-42.49538.5857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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