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- PDB-9csg: Human Serum Albumin Bound to Cerastecin Compound 5e -

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Basic information

Entry
Database: PDB / ID: 9csg
TitleHuman Serum Albumin Bound to Cerastecin Compound 5e
ComponentsAlbumin
KeywordsANTIBIOTIC / HSA / Albumin / MsbA / antibacterial / inhibitor / cerastecin
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / 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 / platelet alpha granule lumen / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / 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
: / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.914 Å
AuthorsHruza, A. / Klein, D.J. / Ishchenko, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii : From Screening Impurity to In Vivo Efficacy.
Authors: Skudlarek, J.W. / Cooke, A.J. / Mitchell, H.J. / Babaoglu, K. / Shaw, A.W. / Tong, L. / Nomland, A.B. / Labroli, M. / Sha, D. / Mulhearn, J.J. / Wu, C. / Li, S.W. / Beshore, D.C. / Hughes, J. ...Authors: Skudlarek, J.W. / Cooke, A.J. / Mitchell, H.J. / Babaoglu, K. / Shaw, A.W. / Tong, L. / Nomland, A.B. / Labroli, M. / Sha, D. / Mulhearn, J.J. / Wu, C. / Li, S.W. / Beshore, D.C. / Hughes, J.M.E. / Jouffroy, M. / Wang, H. / Balibar, C.J. / Painter, R.E. / Shen, P. / Lange, H.S. / Ishchenko, A. / Chen, Y.T. / Klein, D.J. / Tracy, R.W. / Miller, R.R. / Cabalu, T.D. / Wu, Z. / Leithead, A. / Scapin, G. / Hruza, A.W. / Dzhekieva, L. / Bukhtiyarova, M. / Homsher, M.F. / Xu, M. / Bahnck-Teets, C. / McKenney, D. / Buevich, A.V. / Liu, J. / Zhang, L.K. / Meng, T. / Kelly, T. / DiNunzio, E. / Soisson, S. / Cheng, R.K.Y. / Hennig, M. / Raheem, I. / Walker, S.S.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 2, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Oct 16, 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: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4238
Polymers66,2721
Non-polymers2,1517
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.647, 38.624, 97.780
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Albumin


Mass: 66271.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-A1AZR / 2-(4-butylbenzene-1-sulfonamido)-5-(4-{3-carboxy-4-[4-(2-methoxyethyl)benzene-1-sulfonamido]anilino}-4-oxobutanamido)benzoic acid


Mass: 780.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H40N4O11S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25-30% PEG 3350, 50 mM potassium phosphate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→94.5 Å / Num. obs: 30288 / % possible obs: 62.1 % / Redundancy: 6.2 % / CC1/2: 0.998 / Net I/σ(I): 9.5
Reflection shellResolution: 1.91→2.12 Å / Num. unique obs: 1514 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Feb 5data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
BUSTER2.11.8 (23-JAN-2024)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.914→94.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.373 / SU Rfree Blow DPI: 0.238
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT ELECTRON-CLOUD POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1523 5.03 %RANDOM
Rwork0.23 ---
obs0.2316 30288 62.1 %-
Displacement parametersBiso mean: 49.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.8002 Å20 Å23.8614 Å2
2--0.5779 Å20 Å2
3----4.3781 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.914→94.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 142 251 5023
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099599HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8517441HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2863SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1532HARMONIC5
X-RAY DIFFRACTIONt_it4876HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion14.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion606SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8692SEMIHARMONIC4
LS refinement shellResolution: 1.914→2.04 Å
RfactorNum. reflection% reflection
Rfree0.2359 -4.95 %
Rwork0.2974 576 -
obs--7.35 %
Refinement TLS params.Method: refined / Origin x: -23.8686 Å / Origin y: -19.5241 Å / Origin z: -21.0705 Å
111213212223313233
T0.0649 Å20.0086 Å20.0744 Å2--0.1266 Å2-0.0034 Å2---0.1239 Å2
L1.2806 °20.2382 °20.0896 °2-0.0615 °2-0.1816 °2--0.7554 °2
S0.0831 Å °-0.0123 Å °-0.0419 Å °0.0224 Å °-0.0633 Å °0.0472 Å °-0.1452 Å °0.0417 Å °-0.0198 Å °
Refinement TLS groupSelection details: { A|* }

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