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- PDB-8yxb: Crystal structure of the HSA complex with ceftriaxone and myristate -

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Basic information

Entry
Database: PDB / ID: 8yxb
TitleCrystal structure of the HSA complex with ceftriaxone and myristate
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / human serum albumin / antibiotics complex
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/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
Ceftriaxone / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKawai, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20K16060 Japan
CitationJournal: J.Med.Chem. / Year: 2024
Title: Interaction of Cephalosporins with Human Serum Albumin: A Structural Study.
Authors: Kawai, A. / Yamasaki, K. / Otagiri, M. / Doi, Y.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)136,76415
Polymers133,1422
Non-polymers3,62113
Water3,729207
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2687
Polymers66,5711
Non-polymers1,6966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint9 kcal/mol
Surface area28560 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4968
Polymers66,5711
Non-polymers1,9257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint9 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.893, 93.786, 94.747
Angle α, β, γ (deg.)105.730, 100.030, 89.710
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Serum albumin


Mass: 66571.219 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: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N8O7S3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 32% PEG 3350, 50mM potassium phosphate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→45.1 Å / Num. obs: 63358 / % possible obs: 98.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 50.39 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.76
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 10070 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.26 Å / SU ML: 0.3595 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.6258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 3165 5 %
Rwork0.2331 60142 -
obs0.2346 63307 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8855 0 230 207 9292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00149249
X-RAY DIFFRACTIONf_angle_d0.386212485
X-RAY DIFFRACTIONf_chiral_restr0.03311393
X-RAY DIFFRACTIONf_plane_restr0.00331625
X-RAY DIFFRACTIONf_dihedral_angle_d14.9663481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.36031320.32732509X-RAY DIFFRACTION94.19
2.23-2.270.40671360.33322587X-RAY DIFFRACTION96.77
2.27-2.30.3221390.31362639X-RAY DIFFRACTION97.78
2.3-2.340.30291350.28512561X-RAY DIFFRACTION97.75
2.34-2.390.3271360.29012585X-RAY DIFFRACTION97.28
2.39-2.430.30661410.28742673X-RAY DIFFRACTION97.61
2.43-2.480.31221350.28532571X-RAY DIFFRACTION98.08
2.48-2.530.39031360.27772601X-RAY DIFFRACTION97.61
2.54-2.590.33951400.29482646X-RAY DIFFRACTION97.65
2.59-2.660.34111340.29282558X-RAY DIFFRACTION98.57
2.66-2.730.33011380.28932616X-RAY DIFFRACTION97.83
2.73-2.810.29761390.29732633X-RAY DIFFRACTION98.26
2.81-2.90.32291360.28812601X-RAY DIFFRACTION98.49
2.9-3.010.3271400.28332656X-RAY DIFFRACTION98.31
3.01-3.130.3421360.27952583X-RAY DIFFRACTION98.66
3.13-3.270.30371410.26742681X-RAY DIFFRACTION98.81
3.27-3.440.30971350.26942566X-RAY DIFFRACTION98.61
3.44-3.660.28731400.23672656X-RAY DIFFRACTION99.11
3.66-3.940.23651400.22042670X-RAY DIFFRACTION98.87
3.94-4.330.21351390.19892640X-RAY DIFFRACTION98.97
4.33-4.960.22011380.18932622X-RAY DIFFRACTION99.32
4.96-6.240.24551390.21142648X-RAY DIFFRACTION99.36
6.24-38.260.1921400.17032640X-RAY DIFFRACTION98.97
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)
12.74500483495-1.586359123921.274228623424.15456877011-1.667531658072.932811707820.00173752807542-0.0246143312536-0.127105765411-0.1155711159910.00530819683060.0420578275229-0.0500557827466-0.124380955848-0.02667635755490.421681768012-0.03630971144690.04904689489180.314820182125-0.03505052935880.375847817788-2.425-3.423-22.398
20.846714492316-0.981135781514-0.1286488712115.259477811791.593532347671.7266195417-0.164270347501-0.145583299530.07588322822490.2071959664370.205195345762-0.609592147785-0.1592843041060.0963187823007-0.07054478458680.435537749173-0.0183980611727-0.0802976657680.412516290131-0.01531907109690.427601708721.57515.2313.524
31.715537132461.181679990180.1606874264144.862689287170.03175299515162.35941999244-0.0704587089611-0.0662193944921-0.4807810207540.3342227341190.114070197189-0.05603379172910.459963515602-0.191643378091-0.05262852960840.891276993028-0.0393214960613-0.0991437640670.5715256759830.04391862598690.805758864044-6.202-12.43617.231
40.781512137086-0.006157014487430.2900116584081.139715134570.7471008382921.42941010113-0.01801638670270.0203458495324-0.00165002595150.1602228094310.0212566634458-0.1566240744770.0654426147253-0.01166898605486.197008069440.4066366774270.0271472690159-0.04449777413480.3643430383540.02828395140090.46676840889820.20944.752-15.794
51.13580188858-1.02806797744-0.5092235802748.76370897949-0.4620678661531.900540731450.0651513878810.1072167511540.317214104193-0.3456498950030.03337386188810.131684921427-0.509506282312-0.238342292259-0.07795141210230.5051365308390.03325837483360.04835526619970.5436886378920.002552995618110.39810862189413.4951.004-46.908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:173 )A3 - 173
2X-RAY DIFFRACTION2( CHAIN A AND RESID 174:373 )A174 - 373
3X-RAY DIFFRACTION3( CHAIN A AND RESID 374:581 )A374 - 581
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:305 )B3 - 305
5X-RAY DIFFRACTION5( CHAIN B AND RESID 306:584 )B306 - 584

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