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- PDB-7x7x: Human serum albumin complex with deschloro-aripiprazole -

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Basic information

Entry
Database: PDB / ID: 7x7x
TitleHuman serum albumin complex with deschloro-aripiprazole
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / drug complex
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
Chem-AJW / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKawai, A. / Otagiri, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2022
Title: Chlorine Atoms of an Aripiprazole Molecule Control the Geometry and Motion of Aripiprazole and Deschloro-aripiprazole in Subdomain IIIA of Human Serum Albumin.
Authors: Kawai, A. / Kobashigawa, Y. / Hirata, K. / Morioka, H. / Imoto, S. / Nishi, K. / Chuang, V.T.G. / Yamasaki, K. / Otagiri, M.
History
DepositionMar 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1867
Polymers133,1422
Non-polymers1,0445
Water3,711206
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1414
Polymers66,5711
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-5 kcal/mol
Surface area27090 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0463
Polymers66,5711
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-6 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.325, 184.762, 59.542
Angle α, β, γ (deg.)90.000, 106.345, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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-AJW / 7-[4-(4-phenylpiperazin-1-yl)butoxy]-3,4-dihydro-1H-quinolin-2-one


Mass: 379.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 32% PEG 3350, 50mM potassium phosphate pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 70209 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 54.53 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 11184 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YOQ

5yoq


Resolution: 2.1→35.87 Å / SU ML: 0.3093 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.6688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 3510 5 %
Rwork0.2174 66671 -
obs0.2192 70181 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8409 0 71 206 8686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00368674
X-RAY DIFFRACTIONf_angle_d0.585111770
X-RAY DIFFRACTIONf_chiral_restr0.03681330
X-RAY DIFFRACTIONf_plane_restr0.00471541
X-RAY DIFFRACTIONf_dihedral_angle_d14.67563152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.34331350.30722570X-RAY DIFFRACTION94.71
2.13-2.160.34971390.28672642X-RAY DIFFRACTION98.37
2.16-2.190.36971410.27942671X-RAY DIFFRACTION98.53
2.19-2.230.33091390.26222639X-RAY DIFFRACTION98.09
2.23-2.270.30061380.25582614X-RAY DIFFRACTION98.53
2.27-2.30.31261400.24312672X-RAY DIFFRACTION98.49
2.3-2.350.25541380.24482613X-RAY DIFFRACTION98.25
2.35-2.390.28791420.25162700X-RAY DIFFRACTION98.51
2.39-2.440.26731390.2442640X-RAY DIFFRACTION98.76
2.44-2.490.31851400.24392670X-RAY DIFFRACTION98.7
2.49-2.550.25721400.24442658X-RAY DIFFRACTION98.94
2.55-2.620.27761410.24032672X-RAY DIFFRACTION98.84
2.62-2.690.26271410.23272672X-RAY DIFFRACTION98.94
2.69-2.770.27321380.24552637X-RAY DIFFRACTION99.07
2.77-2.850.27711430.26082714X-RAY DIFFRACTION99.06
2.85-2.960.31861420.27322690X-RAY DIFFRACTION99.23
2.96-3.070.31431400.2732664X-RAY DIFFRACTION99.15
3.07-3.210.32021390.26732635X-RAY DIFFRACTION99.11
3.21-3.380.31981410.25332689X-RAY DIFFRACTION99.09
3.38-3.60.27831420.2352690X-RAY DIFFRACTION99.44
3.6-3.870.25391420.20712701X-RAY DIFFRACTION99.65
3.87-4.260.22321420.17982702X-RAY DIFFRACTION99.54
4.26-4.880.20811420.17152697X-RAY DIFFRACTION99.61
4.88-6.140.22911430.20832707X-RAY DIFFRACTION99.41
6.14-35.870.20211430.18242712X-RAY DIFFRACTION98.99
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)
11.486449819340.12622812530.2917572975933.03480482301-0.9468163073922.647487724350.0548341037043-0.0419161548185-0.06183188720160.4045448850360.1078045387770.2751465960050.20976184124-0.112694610292-0.1527475005850.5491026219570.0329052941240.08534175850070.378665337366-0.01004818147720.29538114545913.6012599996-1.6408396400134.1602423435
21.243673399410.141668012564-1.179954032131.591768567010.151386983412.50305266915-0.129070516938-0.0392002811198-0.051034310658-0.03173188022240.267207117719-0.3593560335680.1401346858720.586972511641-0.1266083658590.4922059995620.02005815641450.01369500833070.654274984873-0.09567618340830.50211560536240.4401625838-2.6460683673117.2441838851
34.21108516429-0.8508940799780.2629363568014.781503689981.40487946132.720981294640.1101251291750.6753640100940.159315223435-0.75761938975-0.1507785425760.243634462821-0.3367956781370.1208929480730.03921942577160.645265123830.0329800664093-0.0230274288120.5421161417530.01330062347580.35736531111512.34313913175.926064389713.85421725399
44.49077126447-3.561451981681.73691913793.6268922891-1.446155648617.33095784455-0.39396141749-0.2160096862720.2786876147720.3249247570830.2169419106280.65227817615-0.138761802475-0.802564720570.144208549660.401408650919-0.1188007695430.01661918963970.4833316998410.01198218053940.796310639684-4.2798309303757.412406658716.7962359849
53.00236839346-0.7330218662720.704707809685.776278896480.2412761902192.27306893323-0.0175187571475-0.2476905133630.2616505628170.619879556378-0.1627972887390.459297258306-0.06585041863950.08404655462220.162095585620.474415208998-0.02771189642420.1435546607060.568946866039-0.03491800947210.5277488716581.7366628916257.640249794923.3400251863
63.084072702782.13792160009-0.9474997597576.24155935223-0.9541908221231.76029607277-0.0776764200824-0.0939853005028-0.42759364738-0.03760157942130.06429418888220.1722078889020.302742676503-0.0144572513744-0.009708531038230.3081997583190.00833754994765-3.39879211703E-50.3424022637570.04535835634720.4657309084628.0054856008642.602162836818.4977394837
75.19383244423-1.00567691865-3.041789735181.359050644540.3101090400566.00124704139-0.03107189965380.4982915662250.0442050415343-0.1613900276730.07378432990120.1884192655450.177417222188-0.301021474578-0.04420521423610.465580746991-0.0943391465082-0.06648197832680.5310275016830.03443099938770.46440764268913.747133274851.5818367245-0.0193196490332
84.24082643892-0.296483104671-0.8006157885263.94379284007-1.427232830135.51272590252-0.07057507862260.4968063280880.124044144126-0.1300522731160.111745309422-0.5275471573-0.5440417642710.488111694291-0.01072592778680.552514963419-0.0911253368580.1119365117810.701325475852-0.1378805103810.60065331468636.635100334353.3403190301-2.71109967378
92.46498940336-0.346116587871-0.3989900136115.16303665168-0.964753510114.19142288559-0.0670903994210.0305539610076-0.376716277662-0.058424321439-0.12513010499-0.895055486117-0.0448303940190.3614168792570.1095144854740.355159151771-0.059361532005-0.03009223276870.4518650993020.05158034813950.68932741340832.336846402448.182954001322.7274700786
103.3771933320.355122368631.179631088562.01866525814-1.422783642533.615153801020.338770920137-0.391813257498-1.006116794691.39581839339-0.367418726173-1.315833822030.6435658364390.1219826883460.2311839264191.17091062586-0.0270495907145-0.3150733419910.5368694760770.2064645344870.88944802457928.834306765635.12725754240.8876259967
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 206 )AA1 - 2061 - 196
22chain 'A' and (resid 207 through 398 )AA207 - 398197 - 388
33chain 'A' and (resid 399 through 564 )AA399 - 564389 - 554
44chain 'B' and (resid 3 through 55 )BB3 - 551 - 53
55chain 'B' and (resid 56 through 130 )BB56 - 13054 - 117
66chain 'B' and (resid 131 through 206 )BB131 - 206118 - 193
77chain 'B' and (resid 207 through 292 )BB207 - 292194 - 279
88chain 'B' and (resid 293 through 398 )BB293 - 398280 - 385
99chain 'B' and (resid 399 through 499 )BB399 - 499386 - 486
1010chain 'B' and (resid 500 through 567 )BB500 - 567487 - 551

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