PDB-7qt2: Antibody FenAb208 - fentanyl complex

ID or keywords:

Entry

Database: PDB / ID: 7qt2

Title

Antibody FenAb208 - fentanyl complex

Components

Antibody heavy chain
Antibody light chain

Keywords

IMMUNE SYSTEM / Antibody

Function / homology

Chem-7V7

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.92 Å

Authors

Zeelen, J.P. / Straaten van, M. / Stebbins, C.E.

Funding support

1items

Citation

Journal: Cell Rep / Year: 2023
Title: A trypanosome-derived immunotherapeutics platform elicits potent high-affinity antibodies, negating the effects of the synthetic opioid fentanyl.
Authors: Triller, G. / Vlachou, E.P. / Hashemi, H. / van Straaten, M. / Zeelen, J.P. / Kelemen, Y. / Baehr, C. / Marker, C.L. / Ruf, S. / Svirina, A. / Chandra, M. / Urban, K. / Gkeka, A. / Kruse, S. ...

History

Deposition	Jan 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 24, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7qt2.cif.gz	348.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7qt2.ent.gz	284.3 KB	Display	PDB format
PDBx/mmJSON format	7qt2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7qt2_validation.pdf.gz	991.1 KB	Display	wwPDB validaton report
Full document	7qt2_full_validation.pdf.gz	994.5 KB	Display
Data in XML	7qt2_validation.xml.gz	34.4 KB	Display
Data in CIF	7qt2_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qt/7qt2 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/7qt2	HTTPS FTP

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Related structure data

Related structure data	7qt0SC 7qt3C 7qt4C 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
Related items in Molecule of the Month	#217 - Jan 2018 Opioid Receptors similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Antibody heavy chain

B: Antibody light chain

C: Antibody heavy chain

D: Antibody light chain

hetero molecules

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

1

A: Antibody heavy chain

B: Antibody light chain

hetero molecules

defined by author
Evidence: gel filtration
47.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Antibody heavy chain

D: Antibody light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	153.337, 153.337, 45.986
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

#1: Antibody	Antibody heavy chain Mass: 23715.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293 / Production host: Homo sapiens (human)
#2: Antibody	Antibody light chain Mass: 23737.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide Mass: 336.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₂₈N₂O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.85 Å³/Da / Density % sol: 56.81 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30 % (V/V) PEG400, 0.1 M TEA, 0.2 M MgSO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.92→48.49 Å / Num. obs: 82358 / % possible obs: 99.85 % / Redundancy: 5 % / B_iso Wilson estimate: 33.58 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.08342 / Net I/σ(I): 11.69
Reflection shell	Resolution: 1.92→1.99 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 8154 / CC_1/2: 0.577

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
SCALA		data scaling
PHASER		phasing
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7QT0

7qt0

Resolution: 1.92→48.49 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2301	4124	5 %
R_work	0.1954	78348	-
obs	0.1971	82358	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 123.28 Å² / B_iso mean: 43.2739 Å² / B_iso min: 22.42 Å²

Refinement step

Cycle: final / Resolution: 1.92→48.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6538	0	50	411	6999
B_iso mean	-	-	41.48	44.17	-
Num. residues	-	-	-	-	852

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 29

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.92-1.94	0.4115	134	0.4128	2541	2675	97
1.94-1.96	0.3955	143	0.3822	2723	2866	100
1.96-1.99	0.3846	141	0.3276	2671	2812	100
1.99-2.02	0.293	141	0.2944	2678	2819	100
2.02-2.04	0.3217	140	0.285	2668	2808	100
2.04-2.07	0.3374	142	0.2708	2697	2839	100
2.07-2.1	0.2787	143	0.2586	2705	2848	100
2.1-2.14	0.3294	140	0.2462	2658	2798	100
2.14-2.17	0.275	141	0.2436	2680	2821	100
2.17-2.21	0.2976	141	0.2228	2677	2818	100
2.21-2.25	0.3107	141	0.2571	2685	2826	100
2.25-2.29	0.3055	144	0.275	2732	2876	100
2.29-2.34	0.2669	140	0.2154	2668	2808	100
2.34-2.39	0.261	142	0.2219	2697	2839	100
2.39-2.45	0.2604	143	0.2234	2707	2850	100
2.45-2.51	0.2864	141	0.2265	2683	2824	100
2.51-2.57	0.3167	142	0.2287	2697	2839	100
2.57-2.65	0.2769	142	0.2248	2699	2841	100
2.65-2.74	0.3125	143	0.2106	2707	2850	100
2.74-2.83	0.2219	142	0.205	2697	2839	100
2.83-2.95	0.2709	143	0.204	2710	2853	100
2.95-3.08	0.2454	144	0.2171	2732	2876	100
3.08-3.24	0.2468	141	0.2085	2690	2831	100
3.24-3.45	0.2033	143	0.184	2706	2849	100
3.45-3.71	0.2008	143	0.1655	2723	2866	100
3.71-4.08	0.2101	143	0.1571	2745	2888	100
4.09-4.67	0.1426	145	0.129	2751	2896	100
4.68-5.89	0.1646	146	0.1379	2765	2911	100
5.89-48.49	0.1743	150	0.1781	2856	3006	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	6.9092	1.8952	-6.1544	2.8483	-2.1735	6.8945	-0.2721	0.6019	-0.0962	-0.1287	0.1932	0.2851	0.3711	-0.7767	0.1163	0.2318	-0.0588	-0.0356	0.2066	0.0075	0.4635	38.3984	75.5089	11.0161
2	3.6036	0.3001	-0.4168	2.014	-0.9203	3.8946	-0.0674	-0.1203	-0.1944	-0.0884	-0.0458	0.1127	0.0925	-0.0052	0.1033	0.2189	-0.0182	-0.009	0.1575	0.0093	0.4285	50.4928	74.538	14.1248
3	5.9382	0.6351	-5.2824	2.6798	-0.8718	7.0426	0.1446	0.0361	0.24	0.03	0.0444	0.1254	-0.1526	0.0538	-0.1817	0.1817	-0.0316	-0.0503	0.16	-0.0119	0.3957	45.0642	78.6963	12.7848
4	3.5046	-2.5265	0.7493	8.0961	-2.1095	1.5644	-0.1712	0.098	-0.2394	-0.1479	0.1135	0.1837	-0.014	-0.127	0.055	0.236	-0.0219	0.0248	0.2663	-0.0288	0.4114	17.5882	97.4371	13.1067
5	3.3114	-1.6991	1.2127	4.3112	-2.4186	2.5342	-0.0495	-0.1477	0.4633	0.4572	0.0019	-0.1743	-0.3856	-0.0885	0.0558	0.3114	-0.0448	0.0049	0.2901	-0.0535	0.5336	56.8075	99.3979	17.9989
6	6.3588	0.2543	-1.289	4.997	-0.1341	3.9114	0.0627	0.5047	-0.2235	-0.263	-0.0102	0.6241	-0.0364	-0.3466	-0.0104	0.1963	-0.0068	0.0025	0.1885	0.021	0.4025	50.5989	92.2834	8.8878
7	3.2393	-1.4782	-0.4219	3.1571	-0.8546	1.7267	0.1145	0.2672	0.1214	0.0054	-0.0973	-0.0709	-0.153	0.0128	-0.0052	0.2135	-0.0421	0.0216	0.2219	0.0008	0.5053	57.1623	97.7336	8.228
8	1.2415	0.2565	-0.5778	0.0525	-0.1212	0.2636	0.1385	-0.1757	0.63	0.0205	-0.0646	-0.4768	-0.091	-0.0633	-0.0296	0.2675	-0.026	0.0167	0.2243	-0.0254	0.562	49.5123	98.578	16.719
9	3.0168	1.7005	-3.3417	4.0797	-1.7227	3.7167	-0.1807	-0.0746	-0.1287	0.032	0.1218	0.0003	0.0819	0.0394	0.0285	0.2576	0.0432	0.0038	0.3105	-0.0092	0.5254	20.5028	104.7894	21.5037
10	3.7768	-1.5868	0.6093	3.0559	1.5535	8.8594	-0.3016	-1.3495	-0.3604	0.2729	0.2623	-0.4332	-0.1324	1.0771	-0.002	0.4491	0.0725	0.0151	0.5912	-0.0999	0.6175	24.0816	107.6964	33.4349
11	6.9918	2.8342	-6.9304	4.9928	-4.0409	8.5312	-0.3064	-0.2692	-0.3028	0.217	0.056	-0.2204	0.2404	0.2431	0.3041	0.3058	0.0582	-0.0105	0.3389	0.0011	0.537	24.8066	102.2646	23.6252
12	4.5994	3.382	-1.6098	4.2239	-0.8895	5.1246	-0.2063	-0.3288	0.1006	0.081	0.2472	-0.3431	-0.0968	0.481	0.0117	0.3977	0.0618	0.0575	0.4164	-0.0846	0.722	20.0787	112.0313	29.3113
13	3.9263	0.1336	-0.8923	1.9711	-0.5435	2.1944	0.0912	0.0187	0.0577	-0.0645	-0.018	-0.0969	0.0169	0.0159	-0.0831	0.2583	0.008	0.011	0.1881	0.0316	0.3811	123.6851	151.8613	19.5453
14	5.9644	-2.6848	2.7616	4.6555	-2.245	4.7557	0.1647	-0.1113	-0.4443	-0.3319	0.1813	1.0667	-0.0799	-0.5579	-0.3564	0.2707	0.0588	0.0449	0.2727	-0.086	0.4501	94.3693	165.5794	16.0713
15	3.1189	-0.3419	0.5362	5.694	-2.6257	4.427	0.1234	0.3158	-0.1583	-0.5979	-0.1154	0.1064	0.0367	-0.0923	-0.0086	0.2912	0.033	-0.0114	0.2421	-0.0658	0.39	99.2179	168.3428	10.133
16	3.075	0.0339	-0.4645	3.4357	-1.041	1.9436	-0.0055	0.1963	0.0873	0.1281	-0.0222	0.0702	-0.1387	-0.1411	0.0329	0.2545	-0.0176	0.0454	0.2913	-0.0069	0.4735	131.8193	173.3429	17.8633
17	4.6326	-3.3419	2.1588	4.4932	-1.5721	1.0796	-0.2093	-0.1201	0.1851	0.4298	0.1656	-0.3167	-0.1542	-0.0987	0.0456	0.2695	-0.0223	0.0484	0.303	0.0748	0.3885	125.4678	174.1263	20.7909
18	5.7198	0.234	-1.393	1.9974	-0.012	1.1475	-0.0459	-0.0722	-0.0875	-0.0483	-0.0286	0.2032	0.0045	0.0548	0.0658	0.2571	0.0437	-0.0279	0.2338	0.0126	0.481	94.6123	181.1835	19.4544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 17 )	C	1 - 17
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 18 through 76 )	C	18 - 76
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 77 through 114 )	C	77 - 114
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 115 through 217 )	C	115 - 217
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 1 through 32 )	D	1 - 32
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 33 through 48 )	D	33 - 48
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 49 through 90 )	D	49 - 90
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 91 through 113 )	D	91 - 113
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 114 through 143 )	D	114 - 143
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 144 through 155 )	D	144 - 155
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 156 through 188 )	D	156 - 188
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 189 through 214 )	D	189 - 214
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1 through 114 )	A	1 - 114
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 115 through 137 )	A	115 - 137
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 138 through 216 )	A	138 - 216
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1 through 90 )	B	1 - 90
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 91 through 113 )	B	91 - 113
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 114 through 213 )	B	114 - 213

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