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- PDB-5yb1: Structure and function of human serum albumin-metal agent complex -

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Basic information

Entry
Database: PDB / ID: 5yb1
TitleStructure and function of human serum albumin-metal agent complex
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / albumin / metal complex / pro-drug / drug carrier / target therapy
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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
Chem-8ZR / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.616 Å
AuthorsYang, F. / Wang, T. / Wang, J. / Gou, Y. / Zhang, Z.L.
CitationJournal: Mol. Pharm. / Year: 2018
Title: Developing an Anticancer Copper(II) Multitarget Pro-Drug Based on the His146 Residue in the IB Subdomain of Modified Human Serum Albumin.
Authors: Wang, J. / Gou, Y. / Zhang, Z. / Yu, P. / Qi, J. / Qin, Q. / Sun, H. / Wu, X. / Liang, H. / Yang, F.
History
DepositionSep 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Dec 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,59118
Polymers132,4302
Non-polymers4,16216
Water64936
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2969
Polymers66,2151
Non-polymers2,0818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint2 kcal/mol
Surface area30170 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2969
Polymers66,2151
Non-polymers2,0818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint2 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.492, 95.653, 96.642
Angle α, β, γ (deg.)104.67, 101.43, 89.97
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 / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-8ZR / ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine


Mass: 285.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14CuN4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, MPD, DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.616→33 Å / Num. obs: 38702 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.1
Reflection shellResolution: 2.616→2.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bJ5

1bj5


Resolution: 2.616→33 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.2783 1948 5.03 %
Rwork0.2187 --
obs0.2216 38702 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.616→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9249 0 270 36 9555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059723
X-RAY DIFFRACTIONf_angle_d0.8113064
X-RAY DIFFRACTIONf_dihedral_angle_d14.3356144
X-RAY DIFFRACTIONf_chiral_restr0.0391414
X-RAY DIFFRACTIONf_plane_restr0.0051673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.616-2.68140.36461380.30542574X-RAY DIFFRACTION96
2.6814-2.75390.3881460.31912656X-RAY DIFFRACTION98
2.7539-2.83480.40211330.30252591X-RAY DIFFRACTION98
2.8348-2.92630.43051180.3142689X-RAY DIFFRACTION98
2.9263-3.03080.3171370.29712592X-RAY DIFFRACTION99
3.0308-3.1520.39621600.2992639X-RAY DIFFRACTION99
3.152-3.29530.32851630.28082607X-RAY DIFFRACTION99
3.2953-3.46890.31361380.26912674X-RAY DIFFRACTION99
3.4689-3.68590.30721350.23572632X-RAY DIFFRACTION99
3.6859-3.970.23631520.20892642X-RAY DIFFRACTION99
3.97-4.36860.25011220.17832676X-RAY DIFFRACTION99
4.3686-4.99870.19951300.16952645X-RAY DIFFRACTION99
4.9987-6.28980.26171350.19762662X-RAY DIFFRACTION99
6.2898-31.78260.21971410.15692475X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -9.461 Å / Origin y: -23.6665 Å / Origin z: 15.1391 Å
111213212223313233
T0.3615 Å20.0248 Å2-0.0121 Å2-0.4682 Å2-0.0101 Å2--0.4203 Å2
L0.0449 °20.1415 °2-0.0394 °2-0.7388 °2-0.1747 °2--0.3 °2
S-0.0008 Å °-0.0028 Å °-0.0524 Å °-0.0001 Å °-0.039 Å °-0.2097 Å °0.003 Å °-0.0054 Å °0.0529 Å °
Refinement TLS groupSelection details: all

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