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- PDB-9upd: Crystal structure of human serum albumin complex with nateglinide -

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Basic information

Entry
Database: PDB / ID: 9upd
TitleCrystal structure of human serum albumin complex with nateglinide
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human serum albumin / nateglinide / complex
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 / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / 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
: / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKawai, A. / Nishi, K. / Yamasaki, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Insights into Dual Binding Modes of Nateglinide to Human Serum Albumin.
Authors: Kawai, A. / Nishi, K. / Tokuno, M. / Otagiri, M. / Yamasaki, K.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: 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

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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)133,9676
Polymers133,1422
Non-polymers8254
Water00
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9843
Polymers66,5711
Non-polymers4122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-8 kcal/mol
Surface area26700 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9843
Polymers66,5711
Non-polymers4122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-6 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.450, 180.800, 60.290
Angle α, β, γ (deg.)90.000, 105.640, 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-A1L9H / (2R)-3-phenyl-2-[(4-propan-2-ylcyclohexyl)carbonylamino]propanoic acid / nateglinide


Mass: 317.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H27NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
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: 2.37 Å3/Da / Density % sol: 48.15 %
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 EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.9 Å / Num. obs: 29914 / % possible obs: 99.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.19
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 4737 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.7 Å / SU ML: 0.5086 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2874 1494 5 %
Rwork0.2474 28369 -
obs0.2494 29863 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8401 0 56 0 8457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028636
X-RAY DIFFRACTIONf_angle_d0.43611743
X-RAY DIFFRACTIONf_chiral_restr0.03371354
X-RAY DIFFRACTIONf_plane_restr0.0041541
X-RAY DIFFRACTIONf_dihedral_angle_d12.12053055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.42311310.36282479X-RAY DIFFRACTION95.64
2.89-30.3661360.35792585X-RAY DIFFRACTION100
3-3.120.42381350.37182566X-RAY DIFFRACTION99.89
3.12-3.260.36891360.33252571X-RAY DIFFRACTION99.93
3.26-3.430.36641360.31732595X-RAY DIFFRACTION99.96
3.43-3.650.28351360.27812586X-RAY DIFFRACTION99.96
3.65-3.930.31161360.25712584X-RAY DIFFRACTION99.89
3.93-4.320.24111380.2192614X-RAY DIFFRACTION99.89
4.32-4.950.24361360.21082591X-RAY DIFFRACTION99.96
4.95-6.230.30161360.25412580X-RAY DIFFRACTION99.96
6.23-47.70.23611380.18782618X-RAY DIFFRACTION99.35
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)
11.1725080407-1.082072946030.6760336786521.2250082135-0.08948357408611.59733147102-0.09998719290660.179670474210.0232075859452-0.3623109583650.113294264372-0.00195581253810.3390167944040.0222055695930.0001907598321290.887075652409-0.02509571838850.1448833559870.567995012953-0.04130922964110.4679563337618.75945621074-12.5822105146-7.96866254815
21.25508884383-0.270281903215-0.8198551369581.433764344330.06594911588770.790228719386-0.1638147292690.0543307084423-0.01616557735330.01224081815480.188467806369-0.1607885300920.0650912845426-0.0562373516413-8.51988166126E-50.776951597462-0.0552799102187-0.0113701476210.514878091693-0.01214570333940.4329819632271.677274058572.267567297663.11793057363
31.160961675880.186467219024-0.00627869235672.259218163020.4548247178641.539333789290.0812682607215-0.04159601353250.1131066315410.4781374393860.1880681219240.326029758819-0.2990342404-0.4386228816990.0004011252508440.621123482530.09512500580340.03051124458860.6403610778210.05665017461830.535776218885-19.8850848147-2.7635732235519.3671617777
42.370453238470.6061360909860.1768307384761.86105975033-0.2543599890870.1262828907660.0288181351293-0.3827516403480.3018636111680.23751514639-0.0851988627068-0.1188659793910.1635488931410.0126724437682-4.25049613196E-50.8168845138060.06740228588720.03176021131240.752492512892-0.02686584824530.66360595467312.05688171535.6187728288228.1552467124
51.429869629440.804446969084-0.04485709284520.655513399895-0.3112043024670.381537564546-0.02691922122010.1305684610110.919533245618-0.3409289510110.0553702017281-0.521962919968-0.1713205525570.301824050367-0.0001034112346330.5493724538770.0666879186866-0.07464335983540.651946155754-0.08764358468891.0180115866926.497458035656.263020884317.417427517
60.4952902971410.548707906514-0.02619382138351.06573570595-0.407066195740.312087212724-0.217816822298-0.5105847722010.88501686301-0.3506104781071.04758670611-0.107491980854-0.7246323327230.0935682725540.07181737358420.83387799319-0.05904702634880.05829530495310.924038684972-0.2077460637511.0810476443322.742738581867.555913987314.6187623096
70.2539533580710.439389313659-0.09815271107881.175072587170.0719793545390.1563614631250.128008591610.5006632130280.396204717706-1.14940139057-0.257927734102-0.4926233715190.3222691823750.148354002426-0.0004820098169670.9477852881890.0646573528655-0.1127959692550.888428890297-0.09832592078321.0455599918617.658424221242.38687991354.38794320273
80.6198787622190.234553117534-0.3814368294240.933456078291-0.83504583010.789572073371-0.127642747096-0.1513524095610.00668274903208-0.09008381948370.2066078795420.167818814790.0757544564287-0.1786983703498.74217466709E-50.5310707786280.0376354479904-0.0743577858740.490377592095-0.05101570879910.81124083996114.834145676740.713162957514.1266753316
91.357754624830.000300449818803-0.8790486548391.19202509817-0.1228328027291.193258795250.122829454453-0.3823431737510.02589234410760.3502055377580.04052857050920.09551891404770.129777092240.164415367532-8.07024157006E-50.597782666074-0.0306219595909-0.1079550834560.724739814035-0.007267043538460.7604535063022.1981640421549.66026258836.1824291542
100.49598331988-0.005719661204630.1295441655461.775168964530.6142077771252.954611706130.0105337101615-6.96408854556E-50.0799678509430.0935518305595-0.1989402311770.277415216875-0.222267224231-0.430334978811-0.000497850283710.541364690193-0.02586050930010.01100867568240.6819947792150.1031648618190.881095297598-13.271500567547.651265342118.0624121056
110.2338196262310.12467430674-0.1011943445950.3994022267870.1911450868820.2132305871230.31332404678-0.1990611176670.491260025231-1.00753759049-0.22561724037-0.2765665725580.1151599221360.0913186923750.0002146887742451.07577709462-0.0315403221524-0.07296491810070.7602534644530.004856311336030.768890810288-7.0505333732737.1966237469-6.32553733804
120.07022160837530.296081249512-0.4747570798331.23504389198-1.967780438953.12692203271-0.0347371720111-0.561915803025-0.645799652082-1.3221649119-0.3142228011370.4247794605940.4036552782560.507811453953-0.3699959639481.15335502459-0.19658884076-0.420693800370.939092480537-0.196543655721.24175347936-8.5326225544528.1497291501-11.8476443989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 104 )AA4 - 1041 - 89
22chain 'A' and (resid 105 through 266 )AA105 - 26690 - 251
33chain 'A' and (resid 267 through 398 )AA267 - 398252 - 383
44chain 'A' and (resid 399 through 573 )AA399 - 573384 - 558
55chain 'B' and (resid 1 through 55 )BB1 - 551 - 55
66chain 'B' and (resid 56 through 102 )BB56 - 10256 - 93
77chain 'B' and (resid 103 through 130 )BB103 - 13094 - 121
88chain 'B' and (resid 131 through 204 )BB131 - 204122 - 195
99chain 'B' and (resid 205 through 342 )BB205 - 342196 - 333
1010chain 'B' and (resid 343 through 500 )BB343 - 500334 - 491
1111chain 'B' and (resid 501 through 540 )BB501 - 540492 - 529
1212chain 'B' and (resid 541 through 571 )BB541 - 571530 - 560

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