PDB-9s73: Complex of Equine Serum Albumin with Ampicillin

ID or keywords:

Entry

Database: PDB / ID: 9s73

Title

Complex of Equine Serum Albumin with Ampicillin

Components

Albumin

Keywords

TRANSPORT PROTEIN / serum albumin / 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: 2.5 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	Aug 2, 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	9s73.cif.gz	248.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9s73.ent.gz	201.8 KB	Display	PDB format
PDBx/mmJSON format	9s73.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/s7/9s73 ftp://data.pdbj.org/pub/pdb/validation_reports/s7/9s73	HTTPS FTP

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Related structure data

Related structure data	9q8uC 9qchC 9s42C 9s43C 9sc5C 9sdjC 4f5u 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) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8)

Deposited unit

A: Albumin

hetero molecules

66.8 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)	94.960, 94.960, 143.090
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 , 5 types, 113 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₁₉N₃O₄S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.86 Å³/Da / Density % sol: 57.07 % / Description: Hexagonal column
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.0 M ammonium sulfate, 0.1 M acetate buffer pH 5.0

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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: 2.5→47.53 Å / Num. obs: 25271 / % possible obs: 99.9 % / Redundancy: 5.76 % / CC_1/2: 0.999 / Net I/σ(I): 18.88
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 5.8 % / Num. unique obs: 2778 / CC_1/2: 0.66 / % possible all: 100

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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: 2.5→47.53 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.916 / SU B: 25.546 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26348	1044	4.1 %	RANDOM
R_work	0.20115	-	-	-
obs	0.20362	24227	99.94 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 83.463 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.17 Å²	0.08 Å²	0 Å²
2-	-	0.17 Å²	-0 Å²
3-	-	-	-0.55 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→47.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4559	0	62	101	4722

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.012	4742
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.864	6406
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.712	5	584
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.737	5	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.614	10	849
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	703
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3537
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	6.92	3.913	2322
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	10.416	7.036	2901
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	8.062	4.527	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	16.848	44.53	7224
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: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.364	80	-
R_work	0.333	1791	-
obs	-	-	100 %

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	0.813	1.0528	-0.5458	1.9544	-0.4104	1.5258	0.0886	-0.2706	0.2127	0.2523	-0.2015	0.1392	-0.4772	-0.0064	0.1129	0.6183	0.2244	-0.22	0.3604	-0.2045	0.331	-42.8388	41.1724	24.3239
2	1.2349	-0.7448	1.8681	0.6711	-1.2279	2.9276	-0.3936	-0.8827	0.0743	0.5037	0.3225	-0.1592	-0.5347	-1.1259	0.0711	0.9559	0.3105	-0.1523	1.0844	-0.0861	0.1597	-51.5953	27.6416	36.4886
3	3.9913	0.783	-0.8062	1.6054	-0.7499	0.4127	-0.2513	-0.3554	0.2081	0.6869	0.2982	0.099	-0.2511	-0.0151	-0.0469	0.5935	0.2753	0.077	0.5765	0.005	0.2706	-55.7672	19.5996	29.7881
4	1.4015	-0.9962	1.9156	1.6516	-1.6126	2.7179	0.0183	0.1406	0.273	-0.161	-0.324	-0.2067	0.1809	0.1862	0.3057	0.4854	0.0701	-0.0814	0.4086	0.0654	0.3361	-41.2248	19.5775	9.4997
5	2.0229	-1.9499	0.2189	2.9537	-0.6073	0.1782	-0.0346	0.0215	0.0218	0.0826	0.2461	0.3993	0.0191	-0.0843	-0.2114	0.4961	0.042	-0.1312	0.4152	0.0503	0.3636	-55.7474	20.154	9.3232
6	4.5968	-0.4196	-0.2009	0.7804	-0.654	1.1834	-0.0031	0.2513	0.926	-0.7114	-0.0517	0.2503	0.9438	0.3347	0.0549	1.0148	0.1855	-0.1469	0.4029	0.1317	0.5504	-37.1323	5.1997	-4.0721
7	1.6224	-0.7515	-0.8969	2.1406	0.6492	0.5885	-0.0806	-0.1979	-0.0673	-0.4499	0.1147	-0.0051	0.144	0.2354	-0.034	0.7738	0.1974	-0.0821	0.4975	-0.0207	0.1848	-30.3446	2.3281	3.2614
8	2.0128	0.4156	-3.3918	0.1089	-0.5346	10.35	0.0029	-0.0788	-0.3629	-0.0751	-0.0749	-0.0997	0.3675	-0.079	0.072	0.6386	0.1295	-0.0393	0.2339	0.021	0.3699	-35.8801	-5.4472	15.8274
9	1.6576	0.4092	1.3913	1.9671	-0.7815	1.8984	0.1041	-0.0007	-0.1756	-0.0804	-0.0605	-0.1403	0.1576	-0.0961	-0.0436	0.5403	0.045	-0.0021	0.4389	0.0342	0.2797	-33.4396	2.7294	36.2952
10	2.9983	1.5181	2.4443	2.7207	-0.1281	2.9592	0.0023	-0.0678	0.0276	-0.0838	0.1432	0.1985	0.1017	-0.1321	-0.1455	0.4876	0.0617	-0.0685	0.4398	0.0171	0.3143	-38.7148	8.2393	27.9666
11	3.3693	-0.8821	2.6071	1.7448	-1.6525	3.8924	0.142	0.333	0.2697	-0.2497	-0.3546	-0.216	0.3482	0.4909	0.2127	0.4684	0.1125	0.0121	0.4986	0.0942	0.2854	-23.6922	7.022	26.1381
12	0.2447	0.2399	-0.3681	2.4466	0.1907	0.715	0.1013	0.0004	-0.0065	0.1877	-0.157	-0.0281	-0.0137	0.0164	0.0557	0.5365	0.0143	-0.0024	0.494	0.0431	0.257	-33.6376	7.2046	49.183
13	0.6318	0.5049	-1.2536	1.663	-0.3766	2.9756	0.3	0.05	-0.0873	0.5732	-0.4536	-0.1237	-0.1354	-0.2056	0.1537	0.7196	-0.0423	-0.0045	0.4386	0.0005	0.1878	-35.4844	-0.6621	55.3671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 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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