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- PDB-4iw1: HSA-fructose complex -

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Basic information

Entry
Database: PDB / ID: 4iw1
TitleHSA-fructose complex
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Heart shape / transport
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
beta-D-fructofuranose / D-fructose / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWang, Y. / Yu, H. / Shi, X. / Huang, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural mechanism of ring-opening reaction of glucose by human serum albumin
Authors: Wang, Y. / Yu, H. / Shi, X. / Luo, Z. / Lin, D. / Huang, M.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Structure summary
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0274
Polymers66,5711
Non-polymers4553
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.363, 87.985, 59.350
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Pichia pastoris (fungus) / References: UniProt: P02768
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25%-30% PEG 3350, 50mM potassium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.56→50 Å / Num. all: 18509 / Num. obs: 18509

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO6

1ao6


Resolution: 2.56→48.41 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.88 / SU B: 18.162 / SU ML: 0.388 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 2.587 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31537 954 5.2 %RANDOM
Rwork0.23917 ---
obs0.24341 17539 97 %-
all-18509 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.638 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å2-0 Å22.57 Å2
2---2.67 Å20 Å2
3----1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.56→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 29 3 4312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9716018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9524.667195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1021520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213337
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.4276.1562243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.0039.2212802
X-RAY DIFFRACTIONr_scbond_it6.4646.4412178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.555→2.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 66 -
Rwork0.338 1195 -
obs--91.91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6FRU.paramFRU.top

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