PDB-8fqm: ADC-7 in complex with boronic acid transition state inhibitor MB076

ID or keywords:

Entry

Database: PDB / ID: 8fqm

Title

ADC-7 in complex with boronic acid transition state inhibitor MB076

Components

Beta-lactamase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / BATSI / Acinetobacter-derived Cephalosporinase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Powers, R.A. / Wallar, B.J. / June, C.M. / Fernando, M.C.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.
Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. ...

History

Deposition	Jan 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 26, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 25, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fqm.cif.gz	600.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8fqm_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8fqm_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8fqm_validation.xml.gz	64.7 KB	Display
Data in CIF	8fqm_validation.cif.gz	96.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/8fqm ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fqm	HTTPS FTP

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Related structure data

Related structure data	8fqnC 8fqoC 8fqpC 8fqqC 8fqrC 8fqsC 8fqtC 8fquC 8fqvC 8fqwC 4u0xS S: Starting model for refinement 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	#29 - May 2002 Penicillin-binding Proteins similarity (2) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

165 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

defined by author
Evidence: monomeric biologic assembly
41.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

4

D: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.406, 81.082, 105.442
Angle α, β, γ (deg.)	90.00, 113.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 40808.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-YDB / 1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid Mass: 373.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₂BN₇O₅S₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1339 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.13 Å³/Da / Density % sol: 42.18 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-7 (3.5 mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.53→80.972 Å / Num. obs: 152966 / % possible obs: 91.1 % / Redundancy: 3.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.05 / R_pim(I) all: 0.032 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.53→1.661 Å / R_merge(I) obs: 0.497 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7647 / CC_1/2: 0.704 / R_pim(I) all: 0.369

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1	refinement
Aimless	0.7.1	data scaling
PHASER		phasing
autoPROC	v1.0.5	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x

Resolution: 1.53→56.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2173	7567	4.95 %	0.5
R_work	0.1773	-	-	-
obs	0.1793	152966	74.73 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.53→56.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11035	0	106	1339	12480

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11653
X-RAY DIFFRACTION	f_angle_d	1.047	15919
X-RAY DIFFRACTION	f_dihedral_angle_d	13.207	4261
X-RAY DIFFRACTION	f_chiral_restr	0.064	1750
X-RAY DIFFRACTION	f_plane_restr	0.008	2097

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.53-1.55	0.3326	33	0.2562	454	X-RAY DIFFRACTION	7
1.55-1.57	0.2927	28	0.2406	644	X-RAY DIFFRACTION	10
1.57-1.59	0.2537	48	0.2641	888	X-RAY DIFFRACTION	14
1.59-1.61	0.2828	58	0.2561	1087	X-RAY DIFFRACTION	17
1.61-1.63	0.293	64	0.2515	1384	X-RAY DIFFRACTION	21
1.63-1.65	0.3298	86	0.2509	1818	X-RAY DIFFRACTION	28
1.65-1.67	0.2646	110	0.2503	2283	X-RAY DIFFRACTION	35
1.67-1.7	0.2889	168	0.2384	2882	X-RAY DIFFRACTION	45
1.7-1.72	0.2815	201	0.2481	3661	X-RAY DIFFRACTION	57
1.72-1.75	0.3077	233	0.2369	4386	X-RAY DIFFRACTION	68
1.75-1.78	0.2539	265	0.2318	5392	X-RAY DIFFRACTION	83
1.78-1.82	0.2457	303	0.2178	5817	X-RAY DIFFRACTION	90
1.82-1.85	0.2587	280	0.2197	6170	X-RAY DIFFRACTION	95
1.85-1.89	0.2405	349	0.2206	6306	X-RAY DIFFRACTION	98
1.89-1.93	0.2259	350	0.2104	6415	X-RAY DIFFRACTION	99
1.93-1.97	0.2377	328	0.1996	6408	X-RAY DIFFRACTION	99
1.97-2.02	0.2438	333	0.1937	6423	X-RAY DIFFRACTION	99
2.02-2.08	0.2507	321	0.1861	6422	X-RAY DIFFRACTION	99
2.08-2.14	0.2059	352	0.1768	6418	X-RAY DIFFRACTION	99
2.14-2.21	0.2215	359	0.1731	6366	X-RAY DIFFRACTION	99
2.21-2.29	0.2202	349	0.1743	6297	X-RAY DIFFRACTION	98
2.29-2.38	0.2268	277	0.1818	6218	X-RAY DIFFRACTION	95
2.38-2.49	0.2017	330	0.1799	6199	X-RAY DIFFRACTION	96
2.49-2.62	0.2248	343	0.1849	6461	X-RAY DIFFRACTION	100
2.62-2.78	0.214	315	0.1907	6477	X-RAY DIFFRACTION	99
2.78-3	0.2453	326	0.1874	6453	X-RAY DIFFRACTION	99
3-3.3	0.2173	377	0.1754	6404	X-RAY DIFFRACTION	99
3.3-3.78	0.2144	322	0.1527	6424	X-RAY DIFFRACTION	98
3.78-4.76	0.1642	302	0.1341	6255	X-RAY DIFFRACTION	95
4.76-56.87	0.197	357	0.1652	6587	X-RAY DIFFRACTION	99

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	1.0527	-0.0249	-0.0929	2.2452	0.7373	1.9951	0.0302	-0.0058	-0.0048	-0.0641	-0.0243	0.1229	-0.3518	-0.1565	-0.0076	0.1592	0.0138	-0.0156	0.1007	0.0259	0.1773	3.9217	-0.3821	43.4708
2	3.1426	-0.2744	0.7234	1.5819	-0.941	2.1155	0.073	0.4323	-0.6078	-0.5185	-0.1061	-0.0734	0.4189	0.0822	0.037	0.3222	0.0134	0.0373	0.25	-0.1789	0.4415	14.7443	-29.4626	23.0671
3	1.68	-0.5612	0.8732	1.2078	0.0803	2.356	0.0574	0.2315	-0.2009	-0.3079	0.0821	-0.5044	0.0664	0.4062	-0.1239	0.1696	0.002	0.0583	0.1974	-0.0855	0.4518	20.9567	-22.7083	30.8086
4	1.9184	0.8415	-0.022	2.7306	0.5027	1.8272	0.0054	0.1712	0.0152	-0.388	0.1486	-0.1769	-0.3844	0.0894	-0.1468	0.2118	-0.0123	0.02	0.134	-0.0099	0.1777	9.6792	-3.9083	30.8782
5	4.1544	-1.0371	1.074	2.4619	-2.2784	4.9562	-0.1191	0.254	-0.1593	-0.2504	0.1106	0.4214	0.1184	-0.7876	0.0011	0.1716	-0.0409	-0.0902	0.2891	-0.0364	0.4361	-4.8518	-18.8323	33.101
6	2.0571	-0.4851	-1.5808	3.6874	1.3767	3.3981	0.004	-0.0184	-0.3271	0.2929	-0.0354	0.0453	0.4123	0.0612	0.0379	0.1423	-0.0137	-0.0341	0.1111	0.0182	0.3145	7.0103	-24.2338	44.4284
7	1.2095	-0.4587	-0.4254	1.2209	0.8271	1.1362	0.0033	-0.0262	-0.1447	0.2462	0.0127	-0.296	0.0994	0.0966	-0.0112	0.1779	0.0039	-0.0769	0.1386	0.0556	0.3521	10.7236	-22.8821	50.6368
8	4.0932	2.6437	-0.815	4.043	-0.4877	3.1555	0.0185	-0.0803	-0.1777	-0.0015	0.1323	0.0626	-0.0313	-0.1768	-0.1425	0.0956	0.0097	-0.0326	0.0971	0.0295	0.2422	6.4269	-11.224	44.4586
9	2.1124	1.0579	0.8255	4.3666	-0.6159	4.1599	0.1469	-0.1494	-0.284	0.3152	0.0168	-0.1064	-0.117	-0.0995	-0.1386	0.1522	0.0195	-0.0239	0.071	0.005	0.1648	5.9948	-6.0176	50.2536
10	1.9543	0.3753	-0.5862	1.5151	-0.4559	2.7609	-0.0275	0.0156	0.1589	0.0524	0.0094	0.379	-0.2067	-0.1443	0.0097	0.123	0.004	-0.0275	0.0678	-0.0099	0.1948	-41.2848	2.1976	47.117
11	1.7985	-0.4852	-0.3642	1.9034	0.473	1.7714	-0.0011	0.3516	-0.1101	-0.3094	-0.0345	-0.023	0.0904	0.22	0.0353	0.1608	0.0271	-0.0145	0.2218	-0.0125	0.088	-27.2229	-23.969	27.0441
12	1.2678	0.151	-0.7483	2.3851	0.2108	1.5276	0.0646	0.13	-0.1344	-0.1024	-0.0372	-0.1768	0.1884	0.2973	-0.0153	0.121	0.0428	-0.0043	0.179	-0.017	0.1085	-25.1401	-25.3161	31.8031
13	2.5173	0.5041	-0.521	2.9781	-0.0182	2.4853	0.0077	0.4494	0.1196	-0.4381	-0.0645	0.3425	-0.2092	-0.0857	0.0636	0.2051	0.0091	-0.0758	0.1928	0.0196	0.1512	-40.7344	-10.4023	24.7242
14	0.6719	0.4837	-0.5775	2.0252	0.2311	0.7815	0.0244	0.1108	0.1096	-0.1877	-0.0136	0.1105	-0.1977	0.0435	-0.0147	0.1422	-0.0148	-0.0438	0.1459	0.0322	0.1117	-33.0306	-2.6007	34.5151
15	3.4106	-0.7082	1.6606	2.0182	-0.524	3.576	0.0793	0.0382	-0.1716	-0.0191	-0.072	0.3047	0.2289	-0.1528	-0.006	0.1005	-0.011	0.0194	0.0935	-0.0216	0.1337	-40.8652	-23.5764	41.0618
16	2.4257	-1.0996	-1.2521	1.6415	1.5228	2.0847	-0.051	-0.0502	-0.1467	0.0979	-0.0022	0.0549	0.2117	0.0743	0.0431	0.1228	0.0169	-0.0209	0.091	0.0331	0.0988	-30.9865	-23.4384	50.7028
17	3.4686	1.122	0.4945	4.0639	-0.0049	2.3753	-0.0277	-0.0605	-0.1037	0.0891	0.0378	0.2084	0.0987	-0.0546	-0.0067	0.0653	0.0042	-0.0127	0.073	0.0077	0.0764	-37.6163	-13.0048	45.5031
18	2.6861	1.1144	0.4718	3.2231	-0.6451	3.4491	-0.0276	-0.0891	-0.001	0.1858	0.0049	0.1529	-0.1028	-0.0473	0.0396	0.0807	0.0097	-0.0069	0.0526	-0.0103	0.0925	-37.6873	-7.0314	50.8054
19	0.126	-0.4647	-0.4131	4.8665	-0.4424	2.6702	-0.0782	-0.188	-0.4848	-0.0996	-0.0847	-0.3236	0.7028	0.6112	0.1057	0.6242	0.197	0.1077	0.4258	0.1846	0.4247	19.0248	-36.9451	75.8861
20	2.927	-0.5956	-0.3754	2.1895	-0.2556	1.1338	0.128	-0.6689	-0.0147	-0.0588	0.0108	-0.2781	0.4231	0.6098	-0.1501	0.2922	0.0868	0.0326	0.4425	0.1118	0.2672	21.3377	-21.7	75.0429
21	2.0867	0.5176	-0.5486	1.942	0.0292	0.7101	0.3678	-0.579	0.5859	0.2096	0.1696	-0.264	-0.9306	0.3334	-0.5375	0.6612	-0.1332	0.2314	0.6948	-0.1593	0.428	8.2071	1.3278	91.3638
22	2.7418	0.6331	-1.1786	8.6937	-3.3074	4.9954	0.3414	-0.1022	0.3041	-0.4552	-0.1694	0.229	-0.537	-0.1546	-0.1679	0.3033	0.0893	0.0773	0.3081	0.0384	0.2785	0.707	-3.1951	79.2009
23	1.26	-0.7266	-0.9355	1.2043	0.1499	1.9715	0.1405	-0.7596	0.203	0.1144	0.1309	-0.2071	-0.23	0.5035	-0.2723	0.267	-0.0588	0.0519	0.5933	-0.0081	0.2875	15.0488	-13.3217	82.2517
24	2.426	-1.8905	0.78	3.6629	-0.9897	0.3266	-0.0884	-0.5871	-0.0606	0.2977	0.0577	-0.016	0.2903	0.0154	0.0042	0.3818	0.0922	0.0457	0.8994	0.2144	0.321	3.9643	-24.8511	93.4725
25	0.4488	-0.016	0.043	2.4011	-0.6587	0.6399	-0.0843	-0.7343	-0.2504	0.244	0.097	-0.0162	0.606	0.1159	-0.0783	0.3658	0.1187	0.0102	0.543	0.2046	0.2791	14.3563	-29.0369	82.81
26	1.2022	0.0259	-0.3356	1.0503	-0.0664	0.8106	0.1061	-0.3867	-0.1111	0.4057	-0.0171	-0.1315	0.7277	0.1715	-0.0773	0.4448	0.0291	-0.0374	0.2566	0.0221	0.1132	-22.6994	-28.5996	76.8068
27	1.4991	-0.8867	-0.8534	1.988	0.4133	0.5809	0.0391	-0.2905	0.3492	0.248	-0.0765	0.1593	-0.7982	-0.661	-0.0227	0.6337	0.1894	0.0739	0.7077	-0.1925	0.349	-38.0556	-3.1398	88.2045
28	1.8592	0.459	0.8962	1.6808	0.8881	3.4442	-0.0578	-0.2099	0.3016	0.0505	-0.1155	0.0043	-0.2652	0.1008	0.1707	0.1899	-0.0159	0.0152	0.1652	-0.0152	0.1407	-23.1808	-15.3328	75.7298
29	0.2318	0.0532	0.0638	0.346	0.1276	0.5647	0.303	-0.785	-0.1008	0.5331	-0.2463	0.0935	0.5163	-0.4971	-0.0038	0.5672	-0.3122	0.1413	0.7287	0.0867	-0.1527	-30.8105	-25.1883	90.4235

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 79 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 80 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 166 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 239 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 240 through 256 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 257 through 275 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 276 through 307 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 308 through 329 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 330 through 358 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 62 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 63 through 137 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 166 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 167 through 192 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 193 through 239 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 240 through 275 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 276 through 307 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 308 through 329 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 330 through 358 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 2 through 34 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 35 through 79 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 80 through 111 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 112 through 136 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 137 through 275 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 276 through 307 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 308 through 358 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 3 through 79 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 80 through 166 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 167 through 239 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 240 through 357 )

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