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- PDB-7jwn: Crystal structure of Human Serum Albumin in complex with ketoprofen -

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Basic information

Entry
Database: PDB / ID: 7jwn
TitleCrystal structure of Human Serum Albumin in complex with ketoprofen
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Albumin / HSA / Drug transport / ketoprofen / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule 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
(2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid / CYSTEINE / (R)-Ketoprofen / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCzub, M.P. / Shabalin, I.G. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Iucrj / Year: 2022
Title: Organism-specific differences in the binding of ketoprofen to serum albumin.
Authors: Czub, M.P. / Stewart, A.J. / Shabalin, I.G. / Minor, W.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)68,34210
Polymers66,4561
Non-polymers1,8859
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.499, 38.878, 98.501
Angle α, β, γ (deg.)90.000, 104.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Albumin


Mass: 66456.133 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-9KL / (2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid / Dexketoprofen


Mass: 254.281 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H14O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-JGE / (R)-Ketoprofen


Mass: 254.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 48.28 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Prior to crystallization, the protein at concentration of 162 mg/ml (dissolved in 50 mM Tris pH 7.4 and 20 mM NaCl) was mixed with 100 mM ketoprofen in 100% DMSO in ratio 9:1 (final ...Details: Prior to crystallization, the protein at concentration of 162 mg/ml (dissolved in 50 mM Tris pH 7.4 and 20 mM NaCl) was mixed with 100 mM ketoprofen in 100% DMSO in ratio 9:1 (final ketoprofen concentration 10 mM) and incubated for several hours at 37 oC. Then, 0.2 ul of the protein solution was mixed with 0.2 ul of the well condition (24% PEG 3350, 50 mM K2HPO4 at pH 7.0). The crystallization plate was incubated at RT for 3 months, then for several days at 37 oC, and after the growth of the first HSA crystals, the plate was transferred to RT.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18925 / % possible obs: 96.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Rrim(I) all: 0.092 / Χ2: 0.895 / Net I/av σ(I): 16.9 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.50.8031.38510.6120.4470.9250.79988.5
2.64-2.693.70.6638590.7610.3550.7560.78591.8
2.69-2.743.90.589560.740.3120.6630.82394.5
2.74-2.83.90.5499240.7470.2990.630.83196.6
2.8-2.863.80.4599170.8250.2560.5290.89195.5
2.86-2.9340.4259150.8390.2320.4870.90993.6
2.93-34.30.3899570.8540.2080.4440.86398.2
3-3.084.20.3019290.9030.1660.3460.86497.9
3.08-3.174.40.2549770.9430.1370.290.88398.5
3.17-3.284.40.219510.9320.1150.240.9198.2
3.28-3.394.20.1649610.9680.0910.1880.95598.2
3.39-3.534.10.1299640.9660.0740.1490.9797.2
3.53-3.694.40.1089130.9820.0590.1240.9595.3
3.69-3.884.50.0919810.9780.0510.1050.93498.6
3.88-4.134.30.0769590.990.0410.0870.93598.6
4.13-4.454.30.0659700.9910.0370.0750.91798.2
4.45-4.894.10.0619670.9930.0330.070.8996.3
4.89-5.64.50.0639820.9910.0330.0720.86198.8
5.6-7.054.30.0649700.9830.0360.0740.81396.2
7.05-504.20.06210220.990.0340.0711.03596.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2C

4k2c


Resolution: 2.6→41.92 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 25.679 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The discrepancy in data completeness between the data processing and refinement statistics is caused by the strong anisotropy of diffraction U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ...Details: The discrepancy in data completeness between the data processing and refinement statistics is caused by the strong anisotropy of diffraction U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 772 4.9 %RANDOM
Rwork0.1831 ---
obs0.1855 15048 80.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 51.809 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å2-0.22 Å2
2---0.81 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2.6→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 132 192 4963
Biso mean--41.85 35.55 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134878
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174618
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.6516574
X-RAY DIFFRACTIONr_angle_other_deg1.1111.59810710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0925582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97523.468248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2461524
X-RAY DIFFRACTIONr_chiral_restr0.0440.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021056
LS refinement shellResolution: 2.603→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 18 -
Rwork0.287 365 -
all-383 -
obs--26.88 %
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)
16.1904-0.4623-1.02024.28270.72662.6970.147-0.09180.2857-0.27280.1338-1.0778-0.32140.6578-0.28080.0917-0.10580.11540.2422-0.09780.313451.58821.0629.381
25.84120.1526-0.67474.26331.19466.49350.1843-0.2314-0.0641-0.1643-0.0817-0.14140.20530.073-0.10250.12790.01240.00490.2323-0.04930.149950.8556.33426.451
35.01211.4076-1.022211.36965.07136.2454-0.15790.1605-0.0439-0.34060.3197-0.096-0.08020.2763-0.16180.0196-0.00730.00890.0411-0.00560.012733.01823.14741.937
44.6611.3748-2.8147.9886-2.17128.50090.1165-0.1461-0.0254-0.1485-0.16320.3956-0.7056-0.13230.04670.09090.0065-0.00550.0536-0.0230.038636.06618.11630.765
51.1096-0.4080.25364.18235.76368.7889-0.00140.12410.1064-0.4734-0.20640.1771-0.6483-0.15240.20790.19460.01690.00520.0531-0.0210.126527.43627.06230.734
63.7241-0.9470.636919.1847-4.80276.47590.31810.2774-0.09750.0616-0.2077-0.0980.17550.1178-0.11050.14510.03960.0060.2239-0.06410.028727.13319.7514.524
72.299-0.52371.58841.3974-0.22134.48230.15710.56690.0763-0.334-0.0334-0.361-0.11830.7792-0.12370.27580.09480.12280.3039-0.00980.105538.89223.0256.675
812.79581.96844.46255.17740.284313.6449-0.0634-0.690.09050.4250.2708-0.0026-0.3184-0.4577-0.20730.34630.03550.19590.18950.02810.179636.00234.42613.447
93.74990.701-0.82030.48211.00095.59370.13311.23520.0655-0.18170.070.0571-0.191-0.4053-0.20310.44640.2806-0.07230.6153-0.03350.144615.54621.704-6.461
103.26630.3806-0.26536.7102-4.30125.89670.1746-0.05290.0634-0.1063-0.08450.0441-0.5131-0.1152-0.09010.1883-0.02660.06740.1029-0.06460.05516.59220.47725.935
112.87561.0942-1.39916.5219-2.81827.21940.13140.146-0.1829-0.0706-0.10360.08390.31720.0114-0.02780.11580.0138-0.01990.0237-0.03680.061211.9812.64517.812
122.4706-1.1658-0.84031.13982.84910.5209-0.0295-0.2264-0.35610.03310.04830.12080.0745-0.0592-0.01870.3837-0.0609-0.00950.54320.02450.30536.06815.65144.322
131.574-0.3053-0.27180.2863-0.30873.2073-0.035-0.2949-0.2195-0.0868-0.05030.0345-0.3172-0.93680.08530.32150.1153-0.00360.7417-0.01280.2628-3.08816.35542.917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 58
2X-RAY DIFFRACTION2A59 - 107
3X-RAY DIFFRACTION3A108 - 136
4X-RAY DIFFRACTION4A137 - 155
5X-RAY DIFFRACTION5A156 - 203
6X-RAY DIFFRACTION6A204 - 225
7X-RAY DIFFRACTION7A226 - 271
8X-RAY DIFFRACTION8A272 - 294
9X-RAY DIFFRACTION9A295 - 388
10X-RAY DIFFRACTION10A389 - 438
11X-RAY DIFFRACTION11A439 - 499
12X-RAY DIFFRACTION12A500 - 524
13X-RAY DIFFRACTION13A525 - 2301

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