PDB-4or0: Crystal Structure of Bovine Serum Albumin in complex with naproxen

ID or keywords:

Entry

Database: PDB / ID: 4or0

Title

Crystal Structure of Bovine Serum Albumin in complex with naproxen

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / Bovine Serum Albumin / BSA / Helical protein possessing three domains / Fatty acids / hormones / metabolites / drugs / naproxen / plasma

Function / homology

Function and homology information

cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex ...
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / RIGID BODY REFINEMENT OF THE NATIVE STRUCTURE / Resolution: 2.58 Å

Authors

Zielinski, K. / Bujacz, A. / Sekula, B. / Bujacz, G.

Citation

Journal: Proteins / Year: 2014
Title: Structural studies of bovine, equine, and leporine serum albumin complexes with naproxen.
Authors: Bujacz, A. / Zielinski, K. / Sekula, B.

History

Deposition	Feb 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 4, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4or0.cif.gz	475.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4or0.ent.gz	399.4 KB	Display	PDB format
PDBx/mmJSON format	4or0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4or0_validation.pdf.gz	477.4 KB	Display	wwPDB validaton report
Full document	4or0_full_validation.pdf.gz	509.1 KB	Display
Data in XML	4or0_validation.xml.gz	45.2 KB	Display
Data in CIF	4or0_validation.cif.gz	61.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/4or0 ftp://data.pdbj.org/pub/pdb/validation_reports/or/4or0	HTTPS FTP

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Related structure data

Related structure data	4ot2C 4po0C 4f5sS 4jk4 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5osw-d 4la0-1 2bxb-2 4iw1-d 1e7a-2 1e7b-1 4luh-d 3lu7-1 2bxc-2 3lu6-2 6ocj-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (10) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (9) #37 - Jan 2003 Serum Albumin similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8)

Deposited unit

A: Serum albumin

B: Serum albumin

hetero molecules

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

1

A: Serum albumin

hetero molecules

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

2

B: Serum albumin

hetero molecules

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

Unit cell

Length a, b, c (Å)	216.043, 44.897, 141.699
Angle α, β, γ (deg.)	90.00, 113.99, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Serum albumin / BSA Mass: 66561.969 Da / Num. of mol.: 2 / Fragment: Mature form of BSA / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02769
#2: Chemical	ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN Mass: 230.259 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₄H₁₄O₃ / Comment: antiinflammatory*YM
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% MMEPEG 5000, 0.2M ammonium chloride, 0.1M MES 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.58→50 Å / Num. all: 40202 / Num. obs: 39630 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 64.591 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.07 / Net I/σ(I): 20.46
Reflection shell	Resolution: 2.58→2.68 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.782 / Mean I/σ(I) obs: 2.78 / Num. unique all: 4252 / R_sym value: 0.915 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
DNA		data collection
MOLREP		phasing
REFMAC	5.8.0049	refinement
XDS		data reduction
XDS		data scaling
REFMAC	5.8.0049	phasing

Refinement

Method to determine structure: RIGID BODY REFINEMENT OF THE NATIVE STRUCTURE
Starting model: PDB ENTRY 4F5S

4f5s

Resolution: 2.58→42.28 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.933 / SU B: 28.982 / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.534 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25732	1244	3.1 %	RANDOM
R_work	0.183	-	-	-
all	0.18537	40202	-	-
obs	0.18537	38371	99.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 69.029 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.22 Å²	0 Å²	-1.38 Å²
2-	-	-0.39 Å²	-0 Å²
3-	-	-	0.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.58→42.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9290	0	119	99	9508

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	9637
X-RAY DIFFRACTION	r_angle_refined_deg	2.053	1.99	13033
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.555	5	1162
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.762	24.932	442
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.637	15	1754
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.993	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	1428
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	7204
X-RAY DIFFRACTION	r_mcbond_it	4.069	4.449	4654
X-RAY DIFFRACTION	r_mcangle_it	6.155	6.659	5814
X-RAY DIFFRACTION	r_scbond_it	5.748	4.974	4983
X-RAY DIFFRACTION	r_long_range_B_refined	11.136	38.228	14944

LS refinement shell

Resolution: 2.58→2.647 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	91	-
R_work	0.329	2713	-
obs	-	2713	94.63 %

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	0.2694	0.4967	0.7395	0.9445	1.3979	3.4026	-0.0995	0.0456	-0.0767	-0.2827	0.1113	-0.1125	-0.139	0.5552	-0.0118	0.3255	0.01	-0.0256	0.1492	0.0679	0.1181	9.8605	20.0627	80.9214
2	1.7864	-1.2141	0.9676	2.6289	-0.4011	1.1589	0.0292	0.2844	-0.0229	-0.0868	-0.1545	-0.4402	-0.2438	0.5474	0.1253	0.1904	-0.1858	-0.0452	0.3732	0.117	0.184	23.0702	28.5767	94.9039
3	0.1608	-0.4151	0.2043	2.2158	-0.3172	0.3518	-0.1387	0.0512	0.0498	-0.0072	0.1214	0.1116	-0.2513	0.1661	0.0173	0.2409	-0.1519	-0.0723	0.1896	-0.017	0.1861	16.9001	34.6179	101.6847
4	1.641	-0.6082	-0.5826	1.1612	-0.0075	2.5308	0.0018	-0.0233	-0.0485	-0.1856	-0.1168	0.1042	-0.3077	-0.2705	0.1149	0.1933	0.0516	-0.0779	0.1921	-0.0687	0.1605	-6.1759	24.9486	101.1456
5	2.5084	1.1386	-0.9114	1.802	0.2429	3.6629	-0.0634	-0.0847	0.246	-0.3345	0.0233	-0.0012	-0.6414	-0.1882	0.0402	0.4081	0.1085	-0.1382	0.0506	-0.0686	0.1106	-2.9951	39.2956	99.1488
6	1.8524	2.1558	0.752	4.0073	0.2478	1.4091	0.072	-0.1612	0.1924	0.0828	-0.1938	0.1148	-0.1177	-0.5905	0.1217	0.0926	0.1128	-0.011	0.4443	-0.1328	0.1501	-20.2471	24.5927	114.0014
7	3.5211	-0.4461	-0.8631	0.0969	0.1744	1.9211	0.0541	-0.0623	-0.4126	0.0556	-0.0666	-0.0039	0.0514	-0.5198	0.0125	0.2117	-0.044	-0.0209	0.3925	-0.0006	0.2683	-14.2803	16.7163	117.4596
8	8.7511	1.7369	-0.5684	1.2615	0.4819	0.4402	0.3394	-0.2202	0.3804	0.427	-0.2263	-0.0219	0.2089	-0.0638	-0.1131	0.2201	0.0061	-0.0061	0.2751	0.0084	0.0554	-1.644	19.9391	127.3744
9	2.2826	-2.1917	-2.3231	3.7965	1.7225	2.5369	-0.1763	-0.2584	-0.1098	0.1015	0.1087	0.2132	0.1571	0.24	0.0676	0.1363	0.122	-0.0755	0.2496	0.0651	0.1849	18.0876	12.3673	121.3952
10	2.6026	-0.8131	-0.6685	1.8541	0.7875	0.4212	-0.022	-0.2926	-0.0616	0.0673	0.0395	-0.012	0.0132	0.1178	-0.0175	0.201	0.0517	-0.0433	0.1636	-0.0032	0.1654	11.2552	19.1042	115.3106
11	4.3539	-0.1489	2.2495	0.2082	-0.6277	2.688	0.2893	-0.7902	-0.8742	-0.0252	-0.0418	-0.0186	0.1777	-0.2456	-0.2475	0.2001	0.0052	-0.0314	0.1924	0.1435	0.3751	6.4014	5.799	117.4958
12	4.6155	0.9114	0.1787	2.2444	-1.1836	0.9712	-0.1497	-0.279	0.1164	-0.0098	0.1478	-0.1976	0.0833	-0.0673	0.0019	0.138	0.0786	-0.0428	0.1393	0.028	0.2194	30.8823	9.4846	117.1838
13	5.4702	-0.031	-0.9591	1.485	-0.3043	1.8704	-0.0437	-0.4505	0.3754	0.2924	0.2319	-0.2928	-0.0989	-0.0425	-0.1882	0.1062	0.1369	-0.0667	0.2439	-0.0702	0.149	37.9459	10.7165	125.9447
14	0.5751	-0.0087	1.2418	1.0361	-0.8574	3.4187	0.0067	-0.1929	0.0384	-0.1361	0.104	0.2523	-0.0136	-0.4808	-0.1107	0.2709	-0.0549	-0.0206	0.1461	-0.0519	0.1188	47.1024	28.016	70.0514
15	1.8588	-0.8598	0.2468	1.1721	-0.5697	2.8048	0.1904	-0.5284	-0.099	0.0526	-0.0379	0.2532	0.3504	-0.6125	-0.1525	0.2309	-0.2055	0.0093	0.4665	-0.0174	0.1153	43.919	19.4109	88.9978
16	0.0667	-0.1497	0.1374	0.5462	-0.0836	0.731	0.0187	-0.0515	-0.0462	-0.0301	0.2404	-0.047	0.4181	0.0466	-0.259	0.4621	-0.0455	-0.0732	0.2236	-0.0148	0.1718	52.8268	13.4415	91.1331
17	1.6024	0.7992	0.3386	2.1598	0.7238	1.1351	-0.0596	0.154	-0.1635	-0.0854	0.2989	-0.1829	-0.0208	0.3689	-0.2393	0.1631	0.0388	0.0069	0.2257	-0.1654	0.1381	71.598	23.2763	77.8932
18	3.7766	1.2741	0.3684	2.3827	-0.911	3.2705	0.1967	0.2157	-0.5719	-0.0598	0.2169	-0.0994	0.5429	0.397	-0.4137	0.3916	0.1291	-0.1589	0.1506	-0.1073	0.2147	67.9546	8.8434	77.9292
19	3.2951	2.0033	-1.0982	5.974	0.4088	2.2019	-0.2803	0.029	-0.1595	0.1721	0.4964	-0.8029	0.1146	0.1787	-0.2161	0.0822	0.1302	-0.0872	0.3874	-0.2811	0.2774	90.3086	23.445	81.1035
20	3.5713	0.1798	-0.9316	3.6319	-1.4857	0.9963	0.0835	0.1061	0.314	0.7392	0.1557	-0.2105	-0.2678	0.2008	-0.2391	0.225	0.0678	-0.1512	0.546	-0.3141	0.4203	87.2272	31.4542	87.1605
21	9.174	1.4441	-8.2645	0.8604	-1.7991	7.8924	-0.07	-0.2357	-0.0282	0.1461	-0.0452	-0.2149	-0.0059	0.3093	0.1151	0.2473	0.0056	-0.1482	0.2523	-0.0929	0.1811	82.1186	27.9442	102.4735
22	5.0761	-0.2355	1.2003	5.7513	2.2946	1.2561	0.0408	-0.5576	0.3319	0.5333	0.0499	-0.3521	0.2517	-0.0708	-0.0907	0.3585	0.1038	-0.049	0.238	-0.0724	0.0477	62.4256	35.54	108.4346
23	2.1882	-1.0722	0.4124	2.6796	0.618	1.4877	-0.0341	-0.0741	-0.0104	0.4369	0.1945	-0.0746	0.4556	0.0273	-0.1604	0.3502	0.0699	-0.0949	0.1774	-0.0955	0.1442	64.7951	28.8452	99.492
24	4.3933	0.6493	-1.2611	1.9007	2.3228	4.0171	-0.1402	-0.1532	0.2647	-0.3238	0.6009	-0.1489	-0.3553	0.8678	-0.4607	0.215	-0.0174	-0.0493	0.3041	-0.1213	0.2184	69.9041	42.3856	98.8889
25	2.3932	1.6869	-1.2211	3.8836	-1.6024	1.716	-0.3888	-0.2739	0.1229	-0.0414	0.4786	0.3441	0.3509	0.1601	-0.0898	0.3789	0.0715	0.0325	0.3021	-0.0222	0.2163	49.1162	38.254	111.8622
26	5.6608	1.358	0.0481	1.7953	-0.8311	2.0566	-0.2239	-0.0903	-0.176	0.0084	0.1428	0.0255	0.1872	0.2936	0.081	0.1353	0.1569	-0.0379	0.2059	-0.0217	0.0939	47.3081	36.6354	122.5614

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 106
2	X-RAY DIFFRACTION	2	A	107 - 147
3	X-RAY DIFFRACTION	3	A	148 - 198
4	X-RAY DIFFRACTION	4	A	199 - 250
5	X-RAY DIFFRACTION	5	A	251 - 295
6	X-RAY DIFFRACTION	6	A	296 - 336
7	X-RAY DIFFRACTION	7	A	337 - 366
8	X-RAY DIFFRACTION	8	A	367 - 398
9	X-RAY DIFFRACTION	9	A	399 - 417
10	X-RAY DIFFRACTION	10	A	418 - 468
11	X-RAY DIFFRACTION	11	A	469 - 497
12	X-RAY DIFFRACTION	12	A	498 - 537
13	X-RAY DIFFRACTION	13	A	538 - 583
14	X-RAY DIFFRACTION	14	B	2 - 106
15	X-RAY DIFFRACTION	15	B	107 - 147
16	X-RAY DIFFRACTION	16	B	148 - 198
17	X-RAY DIFFRACTION	17	B	199 - 250
18	X-RAY DIFFRACTION	18	B	251 - 295
19	X-RAY DIFFRACTION	19	B	296 - 336
20	X-RAY DIFFRACTION	20	B	337 - 366
21	X-RAY DIFFRACTION	21	B	367 - 398
22	X-RAY DIFFRACTION	22	B	399 - 417
23	X-RAY DIFFRACTION	23	B	418 - 468
24	X-RAY DIFFRACTION	24	B	469 - 497
25	X-RAY DIFFRACTION	25	B	498 - 537
26	X-RAY DIFFRACTION	26	B	538 - 583

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