PDB-9s42: Complex of Equine Serum Albumin with Hydrolyzed Ampicillin

ID or keywords:

Entry

Database: PDB / ID: 9s42

Title

Complex of Equine Serum Albumin with Hydrolyzed Ampicillin

Components

Albumin

Keywords

TRANSPORT PROTEIN / serum albumin / hydrolyzed ampicillin

Function / homology

Function and homology information

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

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 Å

Authors

Duszynski, K. / Sekula, B. / 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	Jul 25, 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	9s42.cif.gz	246.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9s42.ent.gz	199.1 KB	Display	PDB format
PDBx/mmJSON format	9s42.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/s4/9s42 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/9s42	HTTPS FTP

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Related structure data

Related structure data	9q8uC 9qchC 9s43C 9s73C 9sc5C 9sdjC 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	#258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (10) #37 - Jan 2003 Serum Albumin similarity (10) #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) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Albumin

hetero molecules

66.7 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)	93.470, 93.470, 141.675
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	Albumin Mass: 65854.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

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Non-polymers , 6 types, 145 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-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#5: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.74 Å³/Da / Density % sol: 55.16 % / Description: hexagonal column
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 80% v/v Tacsimate, pH 6.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.32→44.38 Å / Num. obs: 30368 / % possible obs: 99.8 % / Redundancy: 5.14 % / CC_1/2: 0.999 / Net I/σ(I): 15.34
Reflection shell	Resolution: 2.32→2.46 Å / Redundancy: 5.19 % / Num. unique obs: 4884 / CC_1/2: 0.69 / % possible all: 99.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.32→44.38 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.936 / SU B: 19.47 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24579	1520	5 %	RANDOM
R_work	0.17481	-	-	-
obs	0.17837	28879	99.86 %	-

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: 56.594 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.93 Å²	0.47 Å²	0 Å²
2-	-	0.93 Å²	-0 Å²
3-	-	-	-3.03 Å²

Refinement step

Cycle: 1 / Resolution: 2.32→44.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4567	0	59	137	4763

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.012	4745
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.023	1.868	6411
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.293	5	583
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.834	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.737	10	854
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.152	0.2	703
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	3541
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	6.353	3.728	2325
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	8.076	6.698	2903
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	8.978	4.214	2420
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	12.182	40.13	6886
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: 2.32→2.377 Å

	R_factor	Num. reflection	% reflection
R_free	0.374	110	-
R_work	0.315	2107	-
obs	-	-	98.93 %

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	2.796	0.0161	0.6233	2.2564	0.3981	0.7978	0.1382	-0.015	0.2453	-0.3506	0.0541	0.0515	-0.1776	-0.0727	-0.1923	0.2905	-0.099	-0.0064	0.1667	0.0805	0.1612	40.7991	42.0876	70.3602
2	3.6911	0.205	0.2563	2.0875	-0.6125	1.2284	0.1413	0.4529	-0.0793	-0.7062	0.0284	-0.1368	-0.2092	0.1503	-0.1697	0.5117	-0.1448	0.0705	0.2383	0.0391	0.1113	49.6503	28.9014	56.9891
3	4.6686	1.8267	-1.9921	1.7731	-0.3717	2.181	-0.2115	-0.013	-0.4056	-0.3915	0.14	-0.2663	0.0559	0.3644	0.0715	0.1781	-0.0875	0.0379	0.2292	-0.0077	0.0687	54.07	21.1751	63.1235
4	0.9114	1.1573	0.7	1.8125	0.5328	2.1079	-0.0848	-0.0636	0.2337	0.0763	-0.0542	0.2935	-0.0429	0.1345	0.139	0.1971	-0.0145	-0.0506	0.1433	0.0097	0.0996	40.2966	19.5498	83.8321
5	2.18	1.572	0.5128	4.7256	-0.5226	2.2935	-0.0797	0.0998	-0.0565	0.0064	0.0865	-0.3762	-0.0419	0.3651	-0.0068	0.0696	-0.0564	-0.0409	0.2345	-0.0255	0.0688	54.7619	20.2585	83.7692
6	5.2031	1.5615	-0.3786	0.6302	-0.0641	0.3398	0.18	-0.1919	0.1891	0.1562	-0.1387	-0.0317	0.0771	0.0018	-0.0412	0.2123	-0.0011	-0.0572	0.1203	0.0202	0.0597	36.3301	5.064	97.1067
7	3.6597	-0.4812	-2.7523	1.7518	-0.5591	4.8651	0.1712	0.1142	-0.0686	-0.0414	-0.1232	0.2404	-0.017	-0.3162	-0.048	0.1261	-0.0277	-0.0477	0.0862	-0.0151	0.0516	29.4063	2.4838	89.6343
8	1.79	-0.1878	-3.3166	0.0392	0.4564	8.7004	-0.0957	0.0331	-0.194	0.0273	-0.0379	0.0076	0.2301	0.0032	0.1336	0.2015	-0.001	0.0168	0.0936	0.005	0.1316	35.1371	-5.1672	77.2414
9	4.6748	-2.7425	0.2341	1.9441	-0.6782	1.27	0.0824	-0.1461	-0.0355	-0.0348	-0.0552	0.0661	-0.0343	0.1131	-0.0272	0.1772	-0.0154	-0.0248	0.1011	-0.0215	0.0705	32.586	3.1647	56.8504
10	1.3478	-1.1514	1.4858	1.9222	-0.3812	2.5427	0.0171	0.0581	0.0322	-0.0482	-0.0014	-0.0658	0.0995	0.1427	-0.0157	0.1948	-0.0216	-0.0161	0.1871	0.0164	0.0913	37.8452	8.6129	65.1725
11	4.7313	0.4005	2.6293	1.6471	0.4159	4.9949	0.0802	-0.1806	0.2286	0.2236	-0.0987	0.181	0.2371	-0.2194	0.0186	0.0939	-0.0265	0.0116	0.0841	-0.0013	0.0616	23.1393	7.1978	67.1428
12	2.224	-0.1994	-1.7831	1.992	-1.1927	2.972	0.3038	-0.0216	0.1168	-0.2399	-0.1754	0.0718	-0.0518	-0.0834	-0.1283	0.2263	0.0124	0.0065	0.0998	-0.0165	0.0103	32.7077	7.343	44.0258
13	0.9156	0.4004	-0.1544	1.4042	-0.73	3.6594	0.0844	0.008	-0.2112	-0.2968	-0.2383	-0.1304	0.0902	0.1353	0.1539	0.2437	0.0523	0.0081	0.0694	0.0037	0.0658	34.626	-0.5809	37.9591

Refinement TLS group

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