PDB-6nex: Fab fragment of anti-cocaine antibody h2E2

ID or keywords:

Entry

Database: PDB / ID: 6nex

Title

Fab fragment of anti-cocaine antibody h2E2

Components

(Anitgen binding fragment light ...) x 2
Antigen binding fragment heavy chain
Ighg protein

Keywords

IMMUNE SYSTEM / Fab fragment unliganded Fab anti-cocaine antibody reductive methylation

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / FORMIC ACID

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Pokkuluri, P.R. / Tan, K.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2.
Authors: Tan, K. / Zhou, M. / Ahrendt, A.J. / Duke, N.E.C. / Tabaja, N. / Ball, W.J. / Kirley, T.L. / Norman, A.B. / Joachimiak, A. / Schiffer, M. / Wilton, R. / Pokkuluri, P.R.

History

Deposition	Dec 18, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 2.0	Jan 22, 2020	Group: Polymer sequence / Structure summary / Category: entity_poly / struct Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct.title
Revision 2.1	Apr 3, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6nex.cif.gz	406.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6nex.ent.gz	282.1 KB	Display	PDB format
PDBx/mmJSON format	6nex.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6nex_validation.pdf.gz	481.8 KB	Display	wwPDB validaton report
Full document	6nex_full_validation.pdf.gz	491.3 KB	Display
Data in XML	6nex_validation.xml.gz	31.8 KB	Display
Data in CIF	6nex_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/6nex ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6nex	HTTPS FTP

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Related structure data

Related structure data	6nfnC C: citing same article (ref.)
Similar structure data	6co3-d 1nc2-1 1jn6-d 6dg2-1 7lsi-1 4xcn-6 6srv-2 6c5i-d 2ymx-d 2xzq-d 1y18-2 3ls5-d 4xbp-1 4why-1 2fjf-5 6cjk-2 3qhf-d 5i8o-d 2rcs-d 6n16-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

6nfnC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: Anitgen binding fragment light chain

H: Antigen binding fragment heavy chain

A: Anitgen binding fragment light chain

B: Ighg protein

hetero molecules

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

1

L: Anitgen binding fragment light chain

H: Antigen binding fragment heavy chain

hetero molecules

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

2

A: Anitgen binding fragment light chain

B: Ighg protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.787, 128.435, 91.196
Angle α, β, γ (deg.)	90.000, 125.258, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

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Antibody , 4 types, 4 molecules LHAB

#1: Antibody	Anitgen binding fragment light chain Mass: 22913.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal has a pyroglutamate ring PCA: pyroglutamate residue at the N-terminus Lysines are reductively methylated MLY: methylated lysine residue Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): cp
#2: Antibody	Antigen binding fragment heavy chain Mass: 23272.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody	Anitgen binding fragment light chain Mass: 22886.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody	Ighg protein Mass: 23217.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The lysines are reductively methylated MLY: is a reductively methylated lisine Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ighg, AU044919 / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 119 molecules

#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.2 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Wizard II:36 diluted by water (8% PEG3000, 80 mM phosphate-citrate pH 4.2, 160 mM NaCl)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. obs: 54989 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 44.69 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.03 / R_rim(I) all: 0.062 / Χ²: 2.03 / Net I/σ(I): 32.71
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.869 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2694 / CC_1/2: 0.639 / R_pim(I) all: 0.506 / R_rim(I) all: 1.009 / Χ²: 1.83 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHENIX	1.15.2_3472	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: h2E2 Fab-benzoylecgonine complex

Resolution: 2.15→27.77 Å / SU ML: 0.3382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6574

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2536	2754	5.01 %	random
R_work	0.2144	-	-	-
obs	0.2163	54930	97.48 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 73.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→27.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6356	0	19	111	6486

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	6521
X-RAY DIFFRACTION	f_angle_d	0.5995	8906
X-RAY DIFFRACTION	f_chiral_restr	0.0452	1025
X-RAY DIFFRACTION	f_plane_restr	0.0047	1126
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3685	3851

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 (%)
2.15-2.19	0.4234	130	0.3769	2350	X-RAY DIFFRACTION	88.48
2.19-2.23	0.3946	153	0.3629	2589	X-RAY DIFFRACTION	97.06
2.23-2.27	0.3606	133	0.3459	2575	X-RAY DIFFRACTION	97.17
2.27-2.32	0.383	151	0.3429	2580	X-RAY DIFFRACTION	97.54
2.32-2.37	0.3553	141	0.3194	2609	X-RAY DIFFRACTION	97.8
2.37-2.42	0.3672	135	0.307	2653	X-RAY DIFFRACTION	98
2.42-2.48	0.3413	152	0.306	2564	X-RAY DIFFRACTION	97.8
2.48-2.55	0.3313	137	0.3034	2606	X-RAY DIFFRACTION	97.96
2.55-2.63	0.3702	120	0.2908	2667	X-RAY DIFFRACTION	98.34
2.63-2.71	0.3128	120	0.2757	2627	X-RAY DIFFRACTION	98.35
2.71-2.81	0.3046	137	0.2729	2631	X-RAY DIFFRACTION	98.37
2.81-2.92	0.3387	142	0.2648	2649	X-RAY DIFFRACTION	98.52
2.92-3.05	0.2999	144	0.2632	2610	X-RAY DIFFRACTION	98.5
3.05-3.21	0.3289	145	0.2561	2627	X-RAY DIFFRACTION	98.82
3.21-3.41	0.261	166	0.2291	2633	X-RAY DIFFRACTION	98.9
3.41-3.68	0.2575	149	0.2133	2664	X-RAY DIFFRACTION	99.01
3.68-4.05	0.2225	108	0.1904	2676	X-RAY DIFFRACTION	99.11
4.05-4.63	0.1798	132	0.1539	2647	X-RAY DIFFRACTION	98.72
4.63-5.82	0.1792	136	0.1508	2689	X-RAY DIFFRACTION	98.85
5.82-27.77	0.198	123	0.1621	2530	X-RAY DIFFRACTION	92.37

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	2.9088209	0.225671561849	-0.249580579057	2.27810363166	-0.310892347263	3.36058880396	-0.0177543809746	-0.249839854716	-0.110384488103	0.148790407532	0.022893282131	0.0468177485615	0.266977355129	-0.192081452448	-0.0196072651255	0.424967091728	-0.0229912948075	0.0835959202695	0.285577798597	0.0164100590112	0.3107813269	75.0370074858	-129.646403488	114.551767586
2	8.45116589212	-2.42282305241	-3.19446509037	7.06924226719	1.58781541836	3.31813948174	0.499733590956	-0.385021672474	0.859434045458	0.334094234054	-0.192246033434	0.400945969125	-0.790817177726	-0.0555475930809	-0.304107397707	0.824987318207	0.0170233857871	0.0559743236944	0.412820913095	-0.0227782850126	0.574124966712	57.617411608	-96.976715021	119.829634401
3	2.18527297664	-3.02254695204	0.192711171907	6.25812730986	1.14347551749	2.27481766154	0.250461966004	0.17103069808	-0.47695789485	-0.493782409014	-0.354627934438	0.649696303757	0.0327269927149	-0.652688624881	0.11804661347	0.575756805278	-0.138515853164	0.0710348475315	0.455609547464	-0.0238584440454	0.666185650055	51.6512101935	-136.430146346	117.234748143
4	3.23218255187	-1.95076821363	0.0323280379619	5.68445103906	2.11326001694	6.59006172234	-0.0429919979316	-0.137471885335	-0.422925901145	0.283172546419	0.14004563151	0.257108491565	0.330595893801	-0.292625288269	-0.145236304785	0.589088917258	-0.136588989268	0.160030168502	0.451121594445	0.0211366733039	0.612400878402	56.6583911703	-139.993175893	123.385448531
5	6.14141551662	0.114467056523	-3.53102996993	6.12785699024	0.368134065527	6.7494295872	0.186801446559	-0.792082071552	-0.173391880837	1.10664881648	-0.189443419438	0.791154791362	-0.175540366828	-0.0143333578924	0.104830755345	0.628250572914	-0.042825332472	0.200183046965	0.472985742394	0.0629006294557	0.578239977267	54.3277890332	-130.787088975	128.021496088
6	3.31837411542	-2.45747832002	-1.41526178643	4.74984444159	0.262116822346	2.44951426842	-0.608236660129	-0.153723784761	-0.0316248891011	0.710413983288	0.396554143706	0.81210619008	0.265389135484	-0.229288797255	0.121141638547	0.569508168579	-0.034399957195	0.12033999506	0.473309828584	0.0412998427633	0.648790433969	52.2972077606	-125.795184003	121.623616568
7	2.68891191508	-3.18034342302	1.6054905696	5.88061366295	-1.07169775363	1.20832308618	0.486863455484	0.43390661475	0.00285524758094	-0.825766343895	-0.350678092231	0.252024731657	0.164158526418	0.271258251639	0.13660624819	0.924667963288	0.134312397663	-0.103262265337	0.585025287179	-0.0524545872357	0.868302615799	48.7796892595	-95.1427983633	109.935120287
8	3.0460863605	-2.00508185272	0.74135259874	4.62461326176	-1.67214797181	2.69442037576	0.0497451403346	0.0831346751864	0.041472245724	-0.280689056836	-0.010000696373	0.647094741382	0.16953686789	0.0934693925975	-0.093635590371	0.669937807097	0.054079081388	0.0220807504795	0.416267869478	-0.0680324488602	0.692648936081	49.4573247759	-109.019851252	115.111730588
9	6.30269257746	-0.248780452771	-0.17104626185	7.0194202324	-0.656821913461	1.67049212744	0.346088234307	1.37753092451	0.816149002885	-1.636209412	-0.0573062855306	0.607101920464	0.0263900580061	-0.17070861293	0.0593909627494	1.05403761141	0.167874362484	-0.0748207754538	0.689161698246	0.0938188374203	0.783946328646	50.2116907663	-102.348886683	108.252468786
10	7.08243849594	-0.241258748872	0.317775937505	8.41917662976	-3.2702008118	7.39591272525	0.163051729713	0.497746787065	0.539763041266	-1.7377804506	-0.0916308403226	0.942560020663	0.672746674787	-0.546579170053	-0.192350941702	0.783633583071	0.125494612524	-0.188301074823	0.48334744805	-0.119154750494	0.966830500419	40.6562528706	-107.047661419	110.472332955
11	2.88726495744	0.653302536268	1.86300491794	3.86859057788	0.737656749992	5.24763227246	-0.0429622914128	0.310474654216	-0.00664847360355	-0.282195880557	0.0125109791033	0.193804720663	0.295136148765	0.233849451298	0.00769443747546	0.403923247451	-0.00859218965605	0.0655682828171	0.310866249961	0.0402294432248	0.279093128601	27.0823654005	-128.071362737	162.055944109
12	6.3435995342	0.0644713370168	1.31154948106	6.87267295834	-1.15255423349	5.5629948455	-0.00907257121336	-0.189404892872	0.802963030312	-0.371373680872	-0.523477178248	0.813218303897	-0.683945290634	-0.781376662838	0.483933418122	0.929570314163	0.138503582198	-0.168617107071	0.555468138889	-0.112574841627	0.68850865406	20.0610499146	-92.9591753865	151.476723941
13	8.65608816558	-4.77078626465	6.25598728687	8.01329162058	-2.52651022162	8.31559645878	-0.235998335438	1.01659661588	0.332263762686	-1.80454778889	0.0696349089347	0.580184438603	0.10998915928	0.103211940988	0.180295094394	1.04226286256	-0.154811279869	-0.193363463585	0.699819781996	0.126841663905	0.542022945954	22.4483177181	-122.896478368	135.480283022
14	5.3748150843	-0.470775531963	1.07579127053	7.89541685283	0.521523840986	9.61979891558	0.120632354428	0.977286133077	-0.452815558465	-1.57135791343	0.0557498679167	0.124527915327	0.75594695651	0.603252577558	-0.127014204455	0.823331714198	0.0351814540415	-0.0578494994729	0.568269833923	-0.0490814005194	0.357205353326	24.2507761182	-133.962522818	140.374065955
15	5.9816532068	1.12964679084	4.74725262643	7.80697510296	2.93576415917	4.3134887129	-0.35880452082	0.107763923347	-0.145046389829	-1.51118331767	0.145975447391	1.70621644249	0.310561460331	-0.39947643973	0.235778128883	0.759951081229	-0.134175361227	-0.235678339997	0.633949905883	0.061106809705	0.689025749868	15.7563066893	-125.752148342	140.11495565
16	4.07928010398	-3.56509428614	3.22470871257	8.09788477562	-5.04907466765	7.29727309034	0.194857642995	1.19753481943	0.0364372482287	-1.30533435197	-0.392994091967	0.742713130002	-0.022850152419	0.520807381702	0.139260342273	0.751392950398	-0.099638582678	-0.204993575055	0.599188520639	0.0760183900678	0.472429202543	21.3591773977	-119.295725267	140.040329478
17	2.73231381055	-1.51341535605	0.571377334147	3.05778007849	-2.2037756217	1.71886579952	-1.64137923819	0.95306002045	2.27776597158	-1.55379963773	0.092747154556	0.444110011009	-0.754330798314	0.716267400381	1.52679063117	1.21303186883	-0.0672669778764	-0.11710953142	0.614072201762	0.196719791851	0.814831676464	33.1076198163	-88.5179681925	142.836904287
18	3.1834787219	5.24009142848	0.465134662511	9.11899349712	1.46580133394	2.10042997501	-0.137321549534	-0.0189689539772	-0.251180818292	-1.2352016126	0.0913019593234	-0.157094632178	-0.345475772578	-0.221420017524	0.056959643979	1.00886165937	-0.0358959443369	-0.157070808984	0.489622964089	0.178480201858	0.580263496185	27.5125118717	-101.368909686	142.122880053
19	9.33878436246	6.8548927831	5.27858720441	8.69104023796	6.40874540045	5.85480765791	-0.209233777744	1.60879052191	-0.36386054864	-1.57092501097	1.21812359742	-1.49824070246	-0.601442931817	0.505209204394	-0.735186611517	1.58135745493	-0.0521414674036	0.0664875384489	0.65582475731	0.0936653399266	0.724714658684	31.8281870728	-98.2517858761	133.725653508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 116 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 117 through 212 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 2 through 33 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 34 through 83 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 84 through 97 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 99 through 119 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 120 through 134 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 135 through 175 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 176 through 189 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 190 through 214 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 2 through 116 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 117 through 213 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2 through 17 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 18 through 83 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 84 through 97 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 119 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 120 through 134 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 135 through 188 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 189 through 214 )

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Antibody , 4 types, 4 molecules LHAB

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Non-polymers , 4 types, 119 molecules

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