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- PDB-5giy: HSA-Palmitic acid-[RuCl5(ind)]2- -

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Basic information

Entry
Database: PDB / ID: 5giy
TitleHSA-Palmitic acid-[RuCl5(ind)]2-
ComponentsSerum albumin
KeywordsPEPTIDE BINDING PROTEIN / human serum albumin / ruthenium-based drugs / drug delivery systems / interactions of protein-ligand / anticancer activity
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
Chem-7GE / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 Å
AuthorsYang, F. / Wang, T.
Citation
Journal: To Be Published
Title: Structure of HSA-Palmitic acid-[RuCl5(ind)]2-
Authors: Yang, F. / Wang, T.
#1: Journal: European Journal of Medicinal Chemistry / Year: 2014
Title: Structural basis and anticancer properties of ruthenium-based drug complexed with human serum albumin
Authors: Zhang, y. / Ho, A. / Yue, J. / Kong, L. / Zhou, Z. / Wu, X. / Yang, F. / Liang, H.
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 / struct_conn_type
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5469
Polymers66,2151
Non-polymers2,3318
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint14 kcal/mol
Surface area28610 Å2
Unit cell
Length a, b, c (Å)185.845, 38.710, 96.070
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin


Mass: 66214.844 Da / Num. of mol.: 1 / Fragment: UNP residues 27-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Pichia kudriavzevii (yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-7GE / pentakis(chloranyl)-(1~{H}-indazol-2-ium-2-yl)ruthenium(1-)


Mass: 396.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6Cl5N2Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 28 PEG3350, 6% glycerol, 4% DMSO.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47 Å / Num. obs: 22025 / % possible obs: 97 % / Redundancy: 4.3 % / Net I/σ(I): 4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ5

1bj5


Resolution: 2.543→46.429 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 1129 5.13 %
Rwork0.2244 --
obs0.2273 22025 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.543→46.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 128 9 4743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024844
X-RAY DIFFRACTIONf_angle_d0.5236480
X-RAY DIFFRACTIONf_dihedral_angle_d12.11859
X-RAY DIFFRACTIONf_chiral_restr0.02707
X-RAY DIFFRACTIONf_plane_restr0.002834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5433-2.65910.34741230.30362464X-RAY DIFFRACTION94
2.6591-2.79930.34791430.29852627X-RAY DIFFRACTION100
2.7993-2.97460.36051410.30282614X-RAY DIFFRACTION100
2.9746-3.20420.36561270.30212616X-RAY DIFFRACTION100
3.2042-3.52660.31811370.26762635X-RAY DIFFRACTION100
3.5266-4.03660.29311360.23672628X-RAY DIFFRACTION100
4.0366-5.08470.24471650.19152630X-RAY DIFFRACTION100
5.0847-46.43640.24461570.17912682X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 24.9409 Å / Origin y: -0.2294 Å / Origin z: 19.9609 Å
111213212223313233
T0.5928 Å20.0319 Å20.0532 Å2-0.3091 Å20.0517 Å2--0.612 Å2
L1.6701 °20.032 °20.1968 °2--0.01 °20.3225 °2--1.2622 °2
S0.1257 Å °-0.0167 Å °-0.0306 Å °0.0398 Å °-0.0513 Å °-0.0137 Å °-0.1573 Å °-0.198 Å °-0.0027 Å °
Refinement TLS groupSelection details: chain 'A'

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