PDB-5dby: Crystal Structure of Equine Serum Albumin in Complex with Diclofe...

ID or keywords:

Entry

Database: PDB / ID: 5dby

Title

Crystal Structure of Equine Serum Albumin in Complex with Diclofenac and Naproxen Obtained in Displacement Experiment

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / Helical / Three-domain protein /

Serum Albumin / Drugs delivery /

Diclofenac /

Naproxen

Function / homology

Function and homology information

cellular response to calcium ion starvation /

enterobactin binding / negative regulation of mitochondrial depolarization /

toxic substance binding / cellular response to starvation /

fatty acid binding /

pyridoxal phosphate binding /

lipid binding / protein-containing complex /

DNA binding ...
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

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

Funding support

Poland, 3items

Organization	Grant number	Country
Polsih Ministry of Science and Higher Education	N N405 3636 39	Poland
National Science Centre Poland	2013/11/B/ST5/02271	Poland
National Science Centre Poland	2014/12/T/ST5/00136	Poland

Citation

Journal: J.Med.Chem. / Year: 2016
Title: Structural Insights into the Competitive Binding of Diclofenac and Naproxen by Equine Serum Albumin.
Authors: Sekula, B. / Bujacz, A.

History

Deposition	Aug 22, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5dby.cif.gz	246.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/5dby ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dby	HTTPS FTP

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Related structure data

Related structure data	4zbqC 4zbrC 4ot2S 4f5t 4f5u 4j2v C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2ydf-1 6u5a-d 2xvq-2 6ci6-d 6m4r-1 2ydf-2 2xvu-2 171 5id9-d 2vue-2 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	#37 - Jan 2003 Serum Albumin similarity (10) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (10) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Serum albumin

hetero molecules

67.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	94.320, 94.320, 141.690
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

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Protein , 1 types, 1 molecules A

#1: Protein	Serum albumin / Mass: 65625.867 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: blood / References: UniProt: F7BAY6, UniProt: P35747*PLUS

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Non-polymers , 8 types, 101 molecules

#2: Chemical	ChemComp-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC / Diclofenac Mass: 296.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₁Cl₂NO₂ / Comment: antiinflammatory, medication*YM
#3: Chemical	ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN / Naproxen Mass: 230.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₄O₃ / Comment: antiinflammatory*YM
#4: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#6: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#8: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.69 % / Description: hexagonal prism
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.0 M ammonium sulfate, 0.1 M acetate buffer pH 5.0, unliganded crystal was soaked in the diclofenac solution for 1h and transferred to the naproxen solution for 1h

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 6, 2015
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. all: 29716 / Num. obs: 29700 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.09 % / R_merge(I) obs: 0.077 / Net I/σ(I): 15.37
Reflection shell	Resolution: 2.35→2.45 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.989 / Mean I/σ(I) obs: 2.03 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
REFMAC	5.8.0124	phasing
XSCALE	VERSION July 4,2012	data scaling
XDS	VERSION July 4,2012	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OT2

4ot2

Resolution: 2.35→50.01 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.944 / SU B: 23.231 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23397	1121	3.8 %	RANDOM
R_work	0.19332	-	-	-
obs	0.19499	28576	99.93 %	-

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: 58.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	-0.19 Å²	0 Å²
2-	-	-0.39 Å²	-0 Å²
3-	-	-	1.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→50.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4568	0	118	84	4770

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	4790
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	4494
X-RAY DIFFRACTION	r_angle_refined_deg	1.93	2	6461
X-RAY DIFFRACTION	r_angle_other_deg	1.135	3	10452
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.911	5	581
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.852	25	212
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.672	15	849
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.336	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	698
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	5340
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1000
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.602	1.462	2327
X-RAY DIFFRACTION	r_mcbond_other	0.602	1.462	2327
X-RAY DIFFRACTION	r_mcangle_it	0.897	2.171	2900
X-RAY DIFFRACTION	r_mcangle_other	0.897	2.171	2901
X-RAY DIFFRACTION	r_scbond_it	1.045	1.724	2463
X-RAY DIFFRACTION	r_scbond_other	1.045	1.726	2464
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.463	2.522	3561
X-RAY DIFFRACTION	r_long_range_B_refined	5.806	12.875	5402
X-RAY DIFFRACTION	r_long_range_B_other	5.804	12.762	5387
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	67	-
R_work	0.307	2115	-
obs	-	-	99.86 %

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	4.6975	-0.2175	0.958	2.3475	0.8122	2.2909	0.1144	0.1908	0.3069	-0.3353	0.0753	0.1232	-0.3663	-0.1474	-0.1896	0.681	-0.1031	0.0607	0.5469	0.1154	0.1037	41.234	42.165	70.1
2	11.7089	-0.6385	-3.1534	1.3488	0.014	3.1225	0.1377	1.0918	-0.2225	-0.5169	0.1094	-0.4473	0.1079	-0.0173	-0.2471	1.104	-0.1987	0.0735	0.641	-0.0216	0.2498	49.148	29.199	56.375
3	9.6886	1.398	-3.4125	0.7532	-0.3259	4.0479	0.0763	0.333	-0.6903	-0.3622	-0.0182	-0.5348	-0.153	0.4096	-0.0581	0.862	-0.0631	0.2121	0.5412	-0.0038	0.4131	53.728	21.626	62.513
4	1.716	1.606	1.1807	6.291	0.3474	2.4533	0.0826	-0.3694	0.3131	0.2084	-0.149	0.1713	0.042	-0.0399	0.0664	0.5095	-0.0421	-0.0353	0.5421	-0.0453	0.0895	41.459	19.536	84.061
5	1.3026	-2.1549	-0.4737	11.0312	-3.0086	2.9034	0.0117	-0.2191	0.2936	-0.0366	0.0472	-1.1365	-0.0646	0.8083	-0.0588	0.4033	-0.0887	-0.0621	0.7089	-0.1178	0.2773	55.774	20.792	82.939
6	9.0387	3.8875	0.5031	3.7543	-1.9669	2.337	0.49	-0.9363	-0.1308	0.9195	-0.4892	-0.0519	-0.6319	0.0936	-0.0008	0.9426	0.0152	-0.1078	0.6077	0.069	0.0669	37.868	4.748	97.095
7	8.9476	0.6851	-5.3437	4.044	-2.1868	8.8569	-0.0481	0.052	-0.3067	0.4112	0.1324	0.4732	-0.4856	-0.431	-0.0843	0.5553	0.0631	-0.0231	0.4057	0.0118	0.0857	31.046	2.665	89.337
8	3.3816	-0.3482	-7.9807	0.2414	0.0377	21.8702	-0.0736	0.074	-0.1223	-0.0159	-0.0115	0.084	0.3425	-0.2289	0.0851	0.5308	0.0011	0.025	0.4203	0.0156	0.2358	36.101	-5.228	77.127
9	10.9204	-9.2069	-1.5607	7.883	1.8539	3.5379	-0.0137	-0.1379	-0.1939	-0.0112	-0.0338	0.1771	-0.1354	-0.0541	0.0474	0.4988	0.0068	-0.0214	0.5363	-0.0377	0.0074	32.505	2.696	57.161
10	6.0904	-3.5855	2.8044	4.7586	-0.9147	5.1262	0.0926	-0.1271	0.2864	-0.3561	0.0002	-0.5122	0.1301	0.194	-0.0928	0.5385	-0.0453	0.0208	0.4695	-0.0189	0.0637	38.255	8.616	64.806
11	5.7589	-0.4283	1.7958	6.2534	1.1389	4.8663	0.2618	-0.1393	0.0779	0.1344	-0.2768	0.8596	0.5378	-0.56	0.015	0.521	-0.031	-0.0274	0.5038	-0.0279	0.1324	23.911	6.865	67.67
12	6.7821	2.7893	-1.328	4.8214	-0.3277	6.2806	0.3485	0.0487	0.2672	-0.5244	-0.2731	0.0479	-0.8674	-0.1641	-0.0754	0.8615	0.1332	-0.0224	0.4162	-0.0565	0.0247	32.077	6.725	44.296
13	4.8956	1.2977	-1.2635	1.4037	0.0006	5.0168	0.3315	0.1955	-0.022	-0.3247	-0.0237	-0.149	-0.0519	-0.0724	-0.3078	0.9186	0.0419	0.0031	0.4584	-0.0516	0.0459	33.987	-1.086	38.252

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 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

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