PDB-9sdj: Complex of Ovine Serum Albumin with Hydrolyzed Ampicillin

ID or keywords:

Entry

Database: PDB / ID: 9sdj

Title

Complex of Ovine Serum Albumin with Hydrolyzed Ampicillin

Components

Serum albumin

Keywords

TRANSPORT PROTEIN / serum albumin / hydrolyzed ampicillin

Function / homology

Function and homology information

enterobactin binding / blood microparticle / lipid binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Ovis aries (sheep)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Duszynski, K. / Talaj, J.A. / Bujacz, A. / Bujacz, G.

Funding support

Poland, 1items

Citation

Journal: Int J Mol Sci / Year: 2026
Title: Structural Interactions of beta-Lactam Antibiotics with Mammalian Serum Albumins.
Authors: Duszynski, K. / Sekula, B. / Talaj, J. / Bujacz, A.

History

Deposition	Aug 14, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9sdj.cif.gz	249.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9sdj.ent.gz	203.7 KB	Display	PDB format
PDBx/mmJSON format	9sdj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sd/9sdj ftp://data.pdbj.org/pub/pdb/validation_reports/sd/9sdj	HTTPS FTP

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Related structure data

Related structure data	9q8uC 9qchC 9s42C 9s43C 9s73C 9sc5C C: citing same article (ref.)
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 (10) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (9) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Serum albumin

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	121.189, 121.189, 121.965
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 1 molecules A

#1: Protein	Serum albumin Mass: 66427.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P14639

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Non-polymers , 6 types, 80 molecules

#2: Chemical	ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form) Mass: 367.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₂₁N₃O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₂O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.91 Å³/Da / Density % sol: 68.57 % / Description: hexagonal needle
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 80% Tacsimate pH 7.25 and 2% of PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2013 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.55→50 Å / Num. obs: 32992 / % possible obs: 96.7 % / Redundancy: 6.33 % / CC_1/2: 0.999 / R_merge(I) obs: 0.081 / Net I/σ(I): 15.01
Reflection shell	Resolution: 2.55→2.71 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 4387 / CC_1/2: 0.607 / % possible all: 80.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
PDB_EXTRACT		data extraction
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→48.2 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.953 / SU B: 21.845 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21262	1320	4 %	RANDOM
R_work	0.16395	-	-	-
obs	0.16587	31672	96.72 %	-

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: 81.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.13 Å²	0.57 Å²	0 Å²
2-	-	1.13 Å²	-0 Å²
3-	-	-	-3.68 Å²

Refinement step

Cycle: 1 / Resolution: 2.55→48.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4630	0	91	67	4788

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	4840
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.325	1.868	6537
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.73	5	584
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.943	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.18	10	873
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	714
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3643
X-RAY DIFFRACTION	r_gen_planes_other
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	5.961	5.322	2330
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	8.339	9.541	2908
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	10.246	6.162	2510
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	14.964	59.38	7254
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.552→2.619 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.392	70	-
R_work	0.361	1687	-
obs	-	-	70.31 %

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	2.423	-2.0244	0.4671	4.0335	-0.7964	1.9126	0.2511	0.4867	-0.2886	-0.4954	-0.1544	0.276	0.306	-0.2454	-0.0967	0.2498	0.0267	0.0347	0.3451	0.0391	0.1542	46.7739	46.4755	33.6486
2	4.4282	2.1834	-0.3224	4.783	0.8049	1.3055	-0.0295	0.067	0.2325	-0.0451	0.2047	-0.6715	0.1038	0.3415	-0.1752	0.2003	0.0316	0.0475	0.256	-0.0022	0.1904	64.0689	42.01	43.6781
3	2.9494	2.3653	0.208	3.909	-0.4608	1.3662	0.0621	-0.1824	-0.0357	0.2416	-0.0068	-0.7308	-0.1245	0.478	-0.0553	0.2429	0.0342	-0.0018	0.4512	-0.0814	0.3559	62.4105	44.7274	53.7452
4	1.1976	0.0348	0.1897	2.1008	0.3581	3.8736	0.1678	0.0574	0.1797	-0.0088	0.0207	0.1011	0.1733	-0.323	-0.1885	0.0723	0.0285	0.0144	0.1433	0.0473	0.0496	37.8795	42.7037	57.8613
5	3.2328	0.3393	-0.5157	0.8187	-0.2451	3.7852	0.1292	-0.3203	0.5138	0.0982	0.0322	-0.1065	-0.1965	0.3265	-0.1614	0.1576	0.0408	0.0721	0.1784	-0.0539	0.1926	45.883	54.4052	61.242
6	0.9608	-0.7822	1.3235	3.2832	0.6983	3.3711	0.1008	-0.0302	-0.2414	-0.2276	0.0056	0.7002	0.1153	-0.3877	-0.1063	0.2165	-0.0116	-0.0958	0.333	0.0963	0.2907	27.0637	39.0942	74.8294
7	3.0806	-0.7879	1.1847	1.639	0.3498	1.8786	0.1943	-0.0055	-0.2188	0.0351	-0.0045	0.6385	0.4397	-0.1982	-0.1898	0.2893	-0.0772	-0.1175	0.249	0.0897	0.3775	29.4325	29.4024	72.3642
8	10.7292	-1.5129	-0.972	0.9468	0.2609	0.3223	0.0504	-0.2598	-0.127	0.0524	0.0545	0.0694	0.0861	0.0836	-0.1048	0.2385	-0.0212	-0.0234	0.2141	0.037	0.1595	44.0416	24.197	76.3485
9	3.6325	1.5991	-0.7291	4.6945	2.8924	2.7388	-0.0083	-0.2237	0.0704	0.1954	0.1016	-0.0593	0.1521	0.1818	-0.0933	0.3002	0.0507	-0.0607	0.1464	0.0161	0.0475	57.3547	16.0463	61.5175
10	1.9942	-0.5061	-0.1962	3.3759	2.148	3.6584	0.0054	-0.0582	0.0757	-0.2443	0.1164	-0.1222	-0.125	0.1064	-0.1217	0.171	-0.0115	-0.0244	0.1007	0.0105	0.0163	53.1222	26.8164	60.5995
11	0.2685	-0.5658	-0.4424	2.5085	1.3798	0.913	-0.2243	0.0136	-0.1594	0.1885	-0.0958	0.6042	0.2866	-0.1397	0.3201	0.4203	-0.0233	-0.0383	0.3136	0.0317	0.2222	43.564	16.1822	58.7711
12	3.094	-0.9579	-1.0041	1.6506	0.3536	2.4053	-0.2168	-0.039	0.5632	0.1569	0.4687	-0.3496	0.0417	0.4838	-0.2519	0.3782	0.0395	-0.0946	0.253	-0.0823	0.1328	67.7099	11.9594	53.227
13	6.5934	2.43	-3.7554	1.8149	-0.2712	3.8657	-0.0196	-0.5419	-0.2081	0.2873	-0.0339	-0.2621	0.1052	0.4825	0.0535	0.2881	0.1241	-0.1646	0.2864	0.0663	0.2198	75.4405	5.9577	56.9785

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 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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