PDB-8fqs: ADC-212 in complex with boronic acid transition state inhibitor MB076

ID or keywords:

Entry

Database: PDB / ID: 8fqs

Title

ADC-212 in complex with boronic acid transition state inhibitor MB076

Components

Beta-lactamase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / BATSI / inhibitor / Acinetobacter-derived cephalosporinase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

PHOSPHATE ION / Chem-YDB

Function and homology information

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.21 Å

Authors

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

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	8fqs.cif.gz	166.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8fqs.ent.gz	127.6 KB	Display	PDB format
PDBx/mmJSON format	8fqs.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/fq/8fqs ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fqs	HTTPS FTP

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Related structure data

Related structure data	8fqmC 8fqnC 8fqoC 8fqpC 8fqqC 8fqrC 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: monomeric biological assembly

Unit cell

Length a, b, c (Å)	46.483, 71.818, 103.964
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase Mass: 40814.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: 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.: 1 / Source method: obtained synthetically / Formula: C₉H₁₂BN₇O₅S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.17 Å³/Da / Density % sol: 43.2 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M SPG, 25% w/v PEG 1500

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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: 1.0332 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.21→59.09 Å / Num. obs: 75449 / % possible obs: 95 % / Redundancy: 7.3 % / CC_1/2: 0.999 / R_pim(I) all: 0.02 / Net I/σ(I): 15.1
Reflection shell	Resolution: 1.21→1.33 Å / Num. unique obs: 3772 / CC_1/2: 0.682 / R_pim(I) all: 0.383 / % possible all: 66.7

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Processing

Software

Name	Version	Classification
Aimless		data scaling
PHASER		phasing
PHENIX	v1.19	refinement
Coot		model building
autoPROC		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x

Resolution: 1.21→31.21 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1933	3700	4.9 %
R_work	0.1698	-	-
obs	0.1709	75440	69.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.21→31.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2796	0	37	359	3192

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2960
X-RAY DIFFRACTION	f_angle_d	1.214	4028
X-RAY DIFFRACTION	f_dihedral_angle_d	13.975	1105
X-RAY DIFFRACTION	f_chiral_restr	0.096	440
X-RAY DIFFRACTION	f_plane_restr	0.009	523

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 (%)
1.21-1.22	0.3064	1	0.2752	26	X-RAY DIFFRACTION	1
1.22-1.24	0.168	6	0.2831	115	X-RAY DIFFRACTION	3
1.24-1.26	0.3511	22	0.2669	277	X-RAY DIFFRACTION	7
1.26-1.27	0.2259	25	0.2362	478	X-RAY DIFFRACTION	12
1.27-1.29	0.2776	41	0.2314	751	X-RAY DIFFRACTION	19
1.29-1.32	0.2634	43	0.2258	1028	X-RAY DIFFRACTION	26
1.32-1.34	0.2742	86	0.2287	1498	X-RAY DIFFRACTION	39
1.34-1.36	0.2592	108	0.2262	2004	X-RAY DIFFRACTION	51
1.36-1.39	0.297	128	0.2149	2344	X-RAY DIFFRACTION	60
1.39-1.42	0.2341	121	0.2061	2499	X-RAY DIFFRACTION	64
1.42-1.45	0.2349	136	0.2016	2813	X-RAY DIFFRACTION	71
1.45-1.48	0.2121	162	0.2011	3093	X-RAY DIFFRACTION	79
1.48-1.52	0.2265	166	0.1993	3387	X-RAY DIFFRACTION	87
1.52-1.56	0.2107	183	0.1891	3693	X-RAY DIFFRACTION	94
1.56-1.61	0.1718	189	0.1853	3932	X-RAY DIFFRACTION	99
1.61-1.66	0.2276	210	0.1776	3890	X-RAY DIFFRACTION	99
1.66-1.72	0.2059	217	0.1675	3925	X-RAY DIFFRACTION	100
1.72-1.78	0.2038	206	0.1745	3938	X-RAY DIFFRACTION	100
1.78-1.87	0.1954	214	0.1771	3954	X-RAY DIFFRACTION	100
1.87-1.96	0.1878	196	0.1743	3939	X-RAY DIFFRACTION	100
1.96-2.09	0.1892	219	0.1621	3965	X-RAY DIFFRACTION	100
2.09-2.25	0.1875	184	0.1542	3987	X-RAY DIFFRACTION	100
2.25-2.47	0.1904	212	0.1683	3959	X-RAY DIFFRACTION	99
2.47-2.83	0.2008	202	0.1764	3975	X-RAY DIFFRACTION	99
2.83-3.57	0.1951	212	0.1663	4051	X-RAY DIFFRACTION	99
3.57-31.21	0.1661	211	0.1528	4219	X-RAY DIFFRACTION	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	1.7683	0.0076	-0.227	1.9257	0.4115	1.5373	0.0111	-0.0961	0.1251	0.0938	0.0198	-0.126	-0.1135	0.1505	-0.0123	0.0875	-0.0019	0.0009	0.1125	-0.0083	0.1223	11.1153	24.1074	21.7765
2	1.0417	0.2791	-0.1211	1.3024	0.2638	1.8467	-0.0337	0.1091	-0.1274	-0.0455	0.0589	0.004	0.3009	-0.0801	-0.0273	0.1407	-0.0028	-0.0093	0.1028	0.0011	0.112	0.211	-4.5403	7.4977
3	1.037	0.3818	0.0999	2.0887	-0.1684	0.9895	-0.0009	0.1065	0.1802	0.03	0.0516	0.2258	-0.1556	-0.079	-0.0358	0.1333	0.0277	-0.0077	0.135	0.006	0.141	-1.1714	19.4898	12.4855
4	0.8527	0.5878	0.119	1.5269	0.3481	0.0445	-0.0833	0.2168	0.0835	-0.3328	0.0999	0.0961	-0.1272	0.0033	-0.0244	0.1607	0.0002	-0.0108	0.1562	0.0151	0.1287	1.6172	12.3951	5.461
5	0.7932	0.8591	0.1089	1.9784	-0.1237	0.0705	0.1267	-0.156	0.0105	0.3406	-0.112	0.0985	0.0671	0.0045	-0.0189	0.181	-0.0025	0.0131	0.1353	-0.0044	0.122	-0.261	5.3359	28.353
6	0.9642	-0.1396	0.5562	1.4461	0.3822	0.9513	0.0203	0.0408	-0.1921	0.236	-0.009	-0.368	0.2762	0.2646	-0.0193	0.1946	0.0695	-0.0498	0.1612	-0.0027	0.1882	13.3623	-3.983	20.8799
7	0.5493	0.4341	0.6897	1.9575	0.656	1.474	-0.0158	0.0132	-0.1805	0.1282	-0.0149	-0.473	0.2803	0.3022	0.0118	0.1882	0.0988	-0.0224	0.2171	-0.0233	0.2664	19.6798	-2.024	18.8471
8	0.8571	0.1344	0.2044	1.8475	-0.2278	2.0276	0.0515	-0.0866	-0.1109	0.1863	-0.0242	-0.1629	0.1455	0.2481	-0.0255	0.1014	0.0202	-0.019	0.1332	0.0009	0.1284	11.7743	8.5525	21.749
9	1.7904	0.1049	-0.2232	2.018	0.2526	1.4247	0.0268	-0.1493	-0.031	0.2228	0.0423	-0.3274	0.1319	0.2599	-0.0814	0.1171	0.0162	-0.0404	0.1576	-0.0167	0.1587	16.6022	14.5032	23.2367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 6 through 62 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 63 through 176 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 177 through 208 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 209 through 228 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 229 through 257 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 258 through 276 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 277 through 308 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 309 through 330 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 331 through 360 )

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