PDB-9hpv: Crystal structure of OXA-163 in complex with nacubactam (16 hour soak)

ID or keywords:

Entry

Database: PDB / ID: 9hpv

Title

Crystal structure of OXA-163 in complex with nacubactam (16 hour soak)

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / antibiotic resistance / beta lactamase / class D / DBO

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.41 Å

Authors

Hoff, J.F. / Goudar, K.E. / Hinchliffe, P. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: Rsc Med Chem / Year: 2025
Title: Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases.
Authors: Hoff, J.F. / Goudar, K.E. / Calvopina, K. / Beer, M. / Hinchliffe, P. / Shaw, J.M. / Tooke, C.L. / Takebayashi, Y. / Cadzow, A.F. / Harmer, N.J. / Mulholland, A.J. / Schofield, C.J. / Spencer, J.

History

Deposition	Dec 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2025	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hpv.cif.gz	281.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9hpv.ent.gz		Display	PDB format
PDBx/mmJSON format	9hpv.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/hp/9hpv ftp://data.pdbj.org/pub/pdb/validation_reports/hp/9hpv	HTTPS FTP

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Related structure data

Related structure data	9h11C 9h12C 9h13C 9h14C 9h15C 9h16C 9h17C 9h18C 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

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

57.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	122.430, 122.430, 160.470
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22
Space group name Hall	P6₅2(x,y,z+1/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z+1/2 #9: y,x,-z+2/3 #10: -y,-x,-z+1/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+5/6

Components on special symmetry positions

ID	Model	Components
1	1	A-416- HOH
2	1	A-603- HOH
3	1	A-607- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 27912.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaOXA-163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6KZJ2, beta-lactamase

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Non-polymers , 7 types, 518 molecules

#2: Chemical	ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide Mass: 326.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₈N₄O₇S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-A1IYS / (2S,5R)-N-(2-azanylethoxy)-1-methanoyl-5-(oxidanylamino)piperidine-2-carboxamide / nacubactam, reacted form Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₈N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 509 / 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: 3.11 Å³/Da / Density % sol: 60.48 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Tris pH 9.0, 32% PEG 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95 Å / Relative weight: 1
Reflection	Resolution: 1.41→61.21 Å / Num. obs: 135196 / % possible obs: 99.6 % / Redundancy: 38.8 % / CC_1/2: 0.999 / R_pim(I) all: 0.021 / Net I/σ(I): 18.3
Reflection shell	Resolution: 1.41→1.45 Å / Redundancy: 36.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9766 / CC_1/2: 0.376 / R_pim(I) all: 1.022 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.41→48.67 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1704	6587	4.87 %
R_work	0.1584	128537	-
obs	0.1589	135124	99.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 29.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.41→48.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3932	0	145	509	4586

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	4379
X-RAY DIFFRACTION	f_angle_d	0.8401	5934
X-RAY DIFFRACTION	f_chiral_restr	0.0799	613
X-RAY DIFFRACTION	f_plane_restr	0.0079	766
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2249	1650

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 (%)
1.41-1.43	0.3253	229	0.3251	4170	X-RAY DIFFRACTION	98.63
1.43-1.44	0.2912	215	0.3158	4192	X-RAY DIFFRACTION	98.75
1.44-1.46	0.3013	237	0.2982	4163	X-RAY DIFFRACTION	98.72
1.46-1.48	0.313	214	0.2955	4193	X-RAY DIFFRACTION	98.83
1.48-1.5	0.2944	244	0.2854	4158	X-RAY DIFFRACTION	98.81
1.5-1.52	0.2561	228	0.2725	4222	X-RAY DIFFRACTION	99.04
1.52-1.54	0.2711	198	0.274	4214	X-RAY DIFFRACTION	99.01
1.54-1.56	0.2461	242	0.2457	4223	X-RAY DIFFRACTION	99.22
1.56-1.59	0.2096	216	0.2217	4191	X-RAY DIFFRACTION	99.06
1.59-1.61	0.2289	228	0.2181	4237	X-RAY DIFFRACTION	99.38
1.61-1.64	0.2156	198	0.1925	4247	X-RAY DIFFRACTION	99.26
1.64-1.67	0.1907	221	0.1915	4230	X-RAY DIFFRACTION	99.26
1.67-1.7	0.2097	215	0.1803	4246	X-RAY DIFFRACTION	99.55
1.7-1.74	0.1978	219	0.178	4244	X-RAY DIFFRACTION	99.49
1.74-1.78	0.2072	207	0.1764	4253	X-RAY DIFFRACTION	99.55
1.78-1.82	0.1835	229	0.1651	4264	X-RAY DIFFRACTION	99.58
1.82-1.86	0.2046	227	0.1669	4261	X-RAY DIFFRACTION	99.62
1.86-1.91	0.1739	198	0.1721	4299	X-RAY DIFFRACTION	99.62
1.91-1.97	0.1739	231	0.1659	4251	X-RAY DIFFRACTION	99.8
1.97-2.03	0.1731	210	0.1498	4305	X-RAY DIFFRACTION	99.8
2.03-2.11	0.1695	223	0.1485	4300	X-RAY DIFFRACTION	99.87
2.11-2.19	0.1693	190	0.1458	4336	X-RAY DIFFRACTION	99.89
2.19-2.29	0.1771	207	0.1495	4334	X-RAY DIFFRACTION	99.93
2.29-2.41	0.1585	232	0.1522	4313	X-RAY DIFFRACTION	100
2.41-2.56	0.1712	206	0.1518	4353	X-RAY DIFFRACTION	99.98
2.56-2.76	0.1834	218	0.1554	4359	X-RAY DIFFRACTION	100
2.76-3.04	0.1592	216	0.1571	4380	X-RAY DIFFRACTION	100
3.04-3.48	0.1437	227	0.1417	4426	X-RAY DIFFRACTION	100
3.48-4.38	0.1376	217	0.1236	4474	X-RAY DIFFRACTION	99.98
4.38-48.67	0.1475	245	0.147	4699	X-RAY DIFFRACTION	99.96

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	3.88566948905	0.023993573044	3.20818455616	4.10367191071	-0.690480480971	8.29680330474	0.087126401574	0.145833956309	-0.499256070745	0.150495437217	0.0781801910469	-0.234636717985	0.257381871234	0.272805693892	-0.173858865954	0.211668033445	-0.00948158484785	0.0463350074918	0.134254678074	-0.0439859406188	0.276367034118	-52.4861335426	-4.00531631112	-24.9408174063
2	0.932591356249	0.00306718594929	-0.286909868743	2.30809832162	0.493110928718	0.810146955959	-0.0711707939019	0.0438360048691	-0.0332349926398	-0.00973569718769	0.111479435922	0.201819591872	0.0887404035245	-0.0334360895058	-0.0491163907083	0.201357719189	-0.0213777620228	-0.010287427513	0.160997842867	0.014644391006	0.158177821541	-61.9611136466	11.2944046315	-17.3855884792
3	6.09410934257	-1.00273972952	3.8248541088	2.43324840619	-0.690461286971	8.05027429463	-0.0909898735304	-0.406025879188	0.0327092108693	0.388835968926	0.178257334623	-0.0117644429286	-0.32076974437	-0.0154573322848	-0.0508488070141	0.268866450695	-0.0218366420684	0.00324425017447	0.158749892901	-0.021938141665	0.192582000421	-54.182033835	27.7892618752	-7.79016428194
4	4.72449346628	-1.97931575427	-4.54862891023	7.38337455938	-1.31618240016	7.23265914624	-0.023227293948	-0.0247938863496	-0.0667422928982	0.0778722332853	-0.0546595888832	-0.237921682043	-0.0982470066543	0.199221496461	0.0317309282496	0.156412568402	-0.0380099572976	-0.0407985489302	0.146051156184	0.0134094595898	0.142821091662	-50.3913886368	23.8648498918	-11.0969959038
5	5.86528676501	2.09326130577	3.83443821816	3.59312352337	3.01513582792	7.07780360182	-0.079543307699	-0.213608247674	0.160744254101	-0.044372353309	-0.0695869946096	0.263695285814	-0.322349327629	-0.49209606715	0.183614531279	0.156002375917	0.0215391417187	0.0182239152043	0.126043077534	0.046094375692	0.143258450447	-67.8989983989	22.5491234008	-14.0890903221
6	3.08003503495	-0.294497439534	-2.23347959836	2.28642809554	0.731548130884	3.76846511873	-0.157758131264	0.0481625158884	0.00560384026441	0.138539638278	0.0941629632894	0.198308169374	0.113613387949	-0.14951352315	0.0831310763349	0.209828063543	-0.0277100029363	-0.0180536264728	0.164199163129	0.0028268406425	0.173505287445	-65.6303096994	11.0754674629	-17.675294168
7	1.74940030098	-0.36330758449	-0.16526547571	2.49653211861	-0.639665482022	1.59418648572	-0.0764934272356	0.104127427435	-0.0810791988974	-0.00732909314137	0.0923779546382	-0.00525837698243	0.108014010962	-0.135369270905	-0.0413006886489	0.172993446212	-0.0510630232527	0.00262831734772	0.158463319466	-0.00334920308028	0.146463587047	-53.9004639786	16.9038545297	-23.7176062059
8	2.72904370357	0.678914121002	-1.19040553525	3.71162257609	-1.21539838725	4.51126284716	-0.124694003803	-0.0802590519502	-0.225354806012	0.0739731059375	0.0579220986095	-0.367319724166	0.186523797657	0.283509839829	0.0777443612447	0.190430368311	-0.016801694005	-0.00246537713115	0.146703504952	-0.0179953758142	0.217568038683	-48.0723229532	4.52234988646	-20.583535313
9	6.01527295991	-3.41237505146	-2.3446735443	8.63466929242	5.1993251483	5.22859758793	-0.0284019580015	-0.420707952595	0.136703541252	0.446673913149	0.383568658479	-1.24497862403	0.0796743223426	0.622000184744	-0.380666525323	0.263736035634	-0.112682398766	-0.0793618351875	0.366052093576	0.0879732179846	0.421329633516	-22.3170848533	37.4864557455	-21.1005741606
10	3.33627507383	-1.10046805106	-4.55785500725	5.01272260152	3.07944674743	7.68402037218	-0.174237394011	-0.0700214943441	0.149414322554	0.39416516906	0.0428819176919	-0.273206569499	0.0205606859563	0.261888040029	0.119068858626	0.204929740074	-0.064641050181	-0.105024935454	0.189603624055	0.0515753406153	0.224752460275	-28.9027283672	37.6346069576	-22.558391376
11	3.36009392488	2.86465418751	2.06078322155	3.13822792485	1.05910723687	2.67618802019	0.00111550963948	0.0758448992878	0.000169232999503	0.0532407143148	-0.00542331452093	-0.216554847179	-0.0858651776176	0.145422460604	0.0360292448438	0.169807387153	-0.0322017470859	-0.00223855487633	0.168168184281	0.0224278050329	0.177416605022	-34.8721517507	35.7499768923	-37.6516582835
12	4.34350067738	-5.1319093266	-1.18364606824	6.88328424188	1.68500494623	2.82025517238	0.127760537165	0.221445960476	-0.010396695124	-0.288002320587	-0.141934304148	-0.0354273520204	0.327626214236	-0.0860125683413	0.0381446509559	0.252973201689	-0.0788762209095	-0.0170425647491	0.22738293597	-0.0183275687973	0.210347956859	-44.3533711986	19.17235868	-47.6357519444
13	9.54942661561	-3.61300008763	-3.84192446261	1.92933624819	1.74168541692	7.40511169909	0.0173349408193	-0.0942754595546	-0.297176642689	0.00439502263438	-0.0652225505834	-0.0621632262993	0.24985438498	0.0233874494449	0.0543897343328	0.214063027043	-0.0417941526427	-0.00106610502533	0.176736002986	0.0141696334251	0.232021739904	-39.3358722655	17.6369632456	-42.0127629148
14	1.25098982892	-0.429540276411	-0.0901479242224	5.57540302115	1.79395499455	3.11531112448	-0.00158452408224	0.0881825311762	0.0644810295495	-0.257990328191	0.00387761725405	-0.0950034979798	-0.17528110669	-0.0285424930378	-0.00675563698196	0.168799423671	-0.0439337598894	0.00340928831931	0.207095355213	0.0305084742279	0.162205680301	-41.7681519182	36.1603761158	-47.2601170446
15	2.57476632613	0.672143837685	-0.413786316051	1.49510391191	-0.614697453851	2.21900101661	0.00371558752885	0.0904704032791	0.0862062857834	0.0090246756263	0.0368190787721	-0.0138705413746	-0.0721931982202	-0.0512049933177	-0.046270119403	0.178558088168	-0.0218168145364	-0.0169013094561	0.1615249485	0.012412014313	0.168067772129	-42.0237428591	35.6019795736	-35.2595697518
16	2.77576805766	1.31730398317	0.0494070872847	2.33769995857	-0.692625740091	2.37715009898	-0.0262165318498	-0.0134441709903	-0.235085485105	0.0469667463397	-0.0881784684577	-0.401304571749	0.115966913197	0.289218875179	0.108721835835	0.155188312159	-0.0159504268571	-0.0311537925608	0.175137154901	0.0408200514105	0.235193127451	-30.9504722648	27.3288751744	-26.888048513

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 21 through 58 )	A	A	21 - 58	1 - 38
2	2	chain 'A' and (resid 59 through 83 )	A	A	59 - 83	39 - 63
3	3	chain 'A' and (resid 84 through 105 )	A	A	84 - 105	64 - 85
4	4	chain 'A' and (resid 106 through 119 )	A	A	106 - 119	86 - 99
5	5	chain 'A' and (resid 120 through 141 )	A	A	120 - 141	100 - 121
6	6	chain 'A' and (resid 142 through 177 )	A	A	142 - 177	122 - 157
7	7	chain 'A' and (resid 178 through 214 )	A	A	178 - 214	158 - 194
8	8	chain 'A' and (resid 215 through 261 )	A	A	215 - 261	195 - 241
9	9	chain 'B' and (resid 21 through 38 )	B	G	21 - 38	1 - 18
10	10	chain 'B' and (resid 39 through 58 )	B	G	39 - 58	19 - 38
11	11	chain 'B' and (resid 59 through 82 )	B	G	59 - 82	39 - 62
12	12	chain 'B' and (resid 83 through 102 )	B	G	83 - 102	63 - 82
13	13	chain 'B' and (resid 103 through 119 )	B	G	103 - 119	83 - 99
14	14	chain 'B' and (resid 120 through 155 )	B	G	120 - 155	100 - 135
15	15	chain 'B' and (resid 156 through 194 )	B	G	156 - 194	136 - 174
16	16	chain 'B' and (resid 195 through 261 )	B	G	195 - 261	175 - 241

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Protein , 1 types, 2 molecules AB

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Non-polymers , 7 types, 518 molecules

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Protein , 1 types, 2 molecules AB

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