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

ID or keywords:

Entry

Database: PDB / ID: 9upd

Title

Crystal structure of human serum albumin complex with nateglinide

Components

Serum albumin

Keywords

TRANSPORT 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Kawai, A. / Nishi, K. / Yamasaki, K.

Funding support

1items

Citation

Journal: 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

Deposition	Apr 28, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9upd.cif.gz	515.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9upd.ent.gz		Display	PDB format
PDBx/mmJSON format	9upd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9upd_validation.pdf.gz	885 KB	Display	wwPDB validaton report
Full document	9upd_full_validation.pdf.gz	897.5 KB	Display
Data in XML	9upd_validation.xml.gz	43.5 KB	Display
Data in CIF	9upd_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/up/9upd ftp://data.pdbj.org/pub/pdb/validation_reports/up/9upd	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#37 - Jan 2003 Serum Albumin similarity (15) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (15) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (10) #155 - Nov 2012 Vitamin D Receptor similarity (9) #41 - May 2003 Hemoglobin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (2) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #21 - Sep 2001 Antibodies similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#37 - Jan 2003
Serum Albumin
similarity (15)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (15)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (10)
#155 - Nov 2012
Vitamin D Receptor
similarity (9)
#41 - May 2003
Hemoglobin
similarity (1)
#237 - Sep 2019
Nanodiscs and HDL
similarity (2)
#206 - Feb 2017
Globin Evolution
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)

Deposited unit

A: Serum albumin

B: Serum albumin

hetero molecules

134 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serum albumin

hetero molecules

defined by author&software
Evidence: gel filtration
67 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serum albumin

hetero molecules

defined by author&software
67 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#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 interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.15 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.8→48.9 Å / Num. obs: 29914 / % possible obs: 99.4 % / Redundancy: 5.9 % / R_merge(I) obs: 0.073 / Net I/σ(I): 15.19
Reflection shell	Resolution: 2.8→2.97 Å / Redundancy: 5.7 % / R_merge(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

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2874	1494	5 %
R_work	0.2474	28369	-
obs	0.2494	29863	99.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 88.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8401	0	56	0	8457

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	8636
X-RAY DIFFRACTION	f_angle_d	0.436	11743
X-RAY DIFFRACTION	f_chiral_restr	0.0337	1354
X-RAY DIFFRACTION	f_plane_restr	0.004	1541
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1205	3055

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.89	0.4231	131	0.3628	2479	X-RAY DIFFRACTION	95.64
2.89-3	0.366	136	0.3579	2585	X-RAY DIFFRACTION	100
3-3.12	0.4238	135	0.3718	2566	X-RAY DIFFRACTION	99.89
3.12-3.26	0.3689	136	0.3325	2571	X-RAY DIFFRACTION	99.93
3.26-3.43	0.3664	136	0.3173	2595	X-RAY DIFFRACTION	99.96
3.43-3.65	0.2835	136	0.2781	2586	X-RAY DIFFRACTION	99.96
3.65-3.93	0.3116	136	0.2571	2584	X-RAY DIFFRACTION	99.89
3.93-4.32	0.2411	138	0.219	2614	X-RAY DIFFRACTION	99.89
4.32-4.95	0.2436	136	0.2108	2591	X-RAY DIFFRACTION	99.96
4.95-6.23	0.3016	136	0.2541	2580	X-RAY DIFFRACTION	99.96
6.23-47.7	0.2361	138	0.1878	2618	X-RAY DIFFRACTION	99.35

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.1725080407	-1.08207294603	0.676033678652	1.2250082135	-0.0894835740861	1.59733147102	-0.0999871929066	0.17967047421	0.0232075859452	-0.362310958365	0.113294264372	-0.0019558125381	0.339016794404	0.022205569593	0.000190759832129	0.887075652409	-0.0250957183885	0.144883355987	0.567995012953	-0.0413092296411	0.467956333761	8.75945621074	-12.5822105146	-7.96866254815
2	1.25508884383	-0.270281903215	-0.819855136958	1.43376434433	0.0659491158877	0.790228719386	-0.163814729269	0.0543307084423	-0.0161655773533	0.0122408181548	0.188467806369	-0.160788530092	0.0650912845426	-0.0562373516413	-8.51988166126E-5	0.776951597462	-0.0552799102187	-0.011370147621	0.514878091693	-0.0121457033394	0.432981963227	1.67727405857	2.26756729766	3.11793057363
3	1.16096167588	0.186467219024	-0.0062786923567	2.25921816302	0.454824717864	1.53933378929	0.0812682607215	-0.0415960135325	0.113106631541	0.478137439386	0.188068121924	0.326029758819	-0.2990342404	-0.438622881699	0.000401125250844	0.62112348253	0.0951250058034	0.0305112445886	0.640361077821	0.0566501746183	0.535776218885	-19.8850848147	-2.76357322355	19.3671617777
4	2.37045323847	0.606136090986	0.176830738476	1.86105975033	-0.254359989087	0.126282890766	0.0288181351293	-0.382751640348	0.301863611168	0.23751514639	-0.0851988627068	-0.118865979391	0.163548893141	0.0126724437682	-4.25049613196E-5	0.816884513806	0.0674022858872	0.0317602113124	0.752492512892	-0.0268658482453	0.663605954673	12.0568817153	5.61877282882	28.1552467124
5	1.42986962944	0.804446969084	-0.0448570928452	0.655513399895	-0.311204302467	0.381537564546	-0.0269192212201	0.130568461011	0.919533245618	-0.340928951011	0.0553702017281	-0.521962919968	-0.171320552557	0.301824050367	-0.000103411234633	0.549372453877	0.0666879186866	-0.0746433598354	0.651946155754	-0.0876435846889	1.01801158669	26.4974580356	56.2630208843	17.417427517
6	0.495290297141	0.548707906514	-0.0261938213835	1.06573570595	-0.40706619574	0.312087212724	-0.217816822298	-0.510584772201	0.88501686301	-0.350610478107	1.04758670611	-0.107491980854	-0.724632332723	0.093568272554	0.0718173735842	0.83387799319	-0.0590470263488	0.0582953049531	0.924038684972	-0.207746063751	1.08104764433	22.7427385818	67.5559139873	14.6187623096
7	0.253953358071	0.439389313659	-0.0981527110788	1.17507258717	0.071979354539	0.156361463125	0.12800859161	0.500663213028	0.396204717706	-1.14940139057	-0.257927734102	-0.492623371519	0.322269182375	0.148354002426	-0.000482009816967	0.947785288189	0.0646573528655	-0.112795969255	0.888428890297	-0.0983259207832	1.04555999186	17.6584242212	42.3868799135	4.38794320273
8	0.619878762219	0.234553117534	-0.381436829424	0.933456078291	-0.8350458301	0.789572073371	-0.127642747096	-0.151352409561	0.00668274903208	-0.0900838194837	0.206607879542	0.16781881479	0.0757544564287	-0.178698370349	8.74217466709E-5	0.531070778628	0.0376354479904	-0.074357785874	0.490377592095	-0.0510157087991	0.811240839961	14.8341456767	40.7131629575	14.1266753316
9	1.35775462483	0.000300449818803	-0.879048654839	1.19202509817	-0.122832802729	1.19325879525	0.122829454453	-0.382343173751	0.0258923441076	0.350205537758	0.0405285705092	0.0955189140477	0.12977709224	0.164415367532	-8.07024157006E-5	0.597782666074	-0.0306219595909	-0.107955083456	0.724739814035	-0.00726704353846	0.760453506302	2.19816404215	49.660262588	36.1824291542
10	0.49598331988	-0.00571966120463	0.129544165546	1.77516896453	0.614207777125	2.95461170613	0.0105337101615	-6.96408854556E-5	0.079967850943	0.0935518305595	-0.198940231177	0.277415216875	-0.222267224231	-0.430334978811	-0.00049785028371	0.541364690193	-0.0258605093001	0.0110086756824	0.681994779215	0.103164861819	0.881095297598	-13.2715005675	47.6512653421	18.0624121056
11	0.233819626231	0.12467430674	-0.101194344595	0.399402226787	0.191145086882	0.213230587123	0.31332404678	-0.199061117667	0.491260025231	-1.00753759049	-0.22561724037	-0.276566572558	0.115159922136	0.091318692375	0.000214688774245	1.07577709462	-0.0315403221524	-0.0729649181007	0.760253464453	0.00485631133603	0.768890810288	-7.05053337327	37.1966237469	-6.32553733804
12	0.0702216083753	0.296081249512	-0.474757079833	1.23504389198	-1.96778043895	3.12692203271	-0.0347371720111	-0.561915803025	-0.645799652082	-1.3221649119	-0.314222801137	0.424779460594	0.403655278256	0.507811453953	-0.369995963948	1.15335502459	-0.19658884076	-0.42069380037	0.939092480537	-0.19654365572	1.24175347936	-8.53262255445	28.1497291501	-11.8476443989

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 4 through 104 )	A	A	4 - 104	1 - 89
2	2	chain 'A' and (resid 105 through 266 )	A	A	105 - 266	90 - 251
3	3	chain 'A' and (resid 267 through 398 )	A	A	267 - 398	252 - 383
4	4	chain 'A' and (resid 399 through 573 )	A	A	399 - 573	384 - 558
5	5	chain 'B' and (resid 1 through 55 )	B	B	1 - 55	1 - 55
6	6	chain 'B' and (resid 56 through 102 )	B	B	56 - 102	56 - 93
7	7	chain 'B' and (resid 103 through 130 )	B	B	103 - 130	94 - 121
8	8	chain 'B' and (resid 131 through 204 )	B	B	131 - 204	122 - 195
9	9	chain 'B' and (resid 205 through 342 )	B	B	205 - 342	196 - 333
10	10	chain 'B' and (resid 343 through 500 )	B	B	343 - 500	334 - 491
11	11	chain 'B' and (resid 501 through 540 )	B	B	501 - 540	492 - 529
12	12	chain 'B' and (resid 541 through 571 )	B	B	541 - 571	530 - 560

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