PDB-9hxo: A01 mAbs bound to cobratoxin at pH 6.0

ID or keywords:

Entry

Database: PDB / ID: 9hxo

Title

A01 mAbs bound to cobratoxin at pH 6.0

Components

Alpha-cobratoxin
heavy chain
light chain

Keywords

TOXIN / cobratoxin / mAB / pH sensitivity

Function / homology

Function and homology information

acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Naja kaouthia (monocled cobra)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.49 Å

Authors

Wade, J.W. / Bohn, M.F. / Laustsen, A.H. / Morth, J.P.

Funding support

Denmark, 1items

Citation

Journal: Mabs / Year: 2025
Title: Rational design of antibodies with pH-dependent antigen-binding properties using structural insights from broadly neutralizing antibodies against alpha-neurotoxins.
Authors: Wade, J. / Strancar, N. / Fernandez-Quintero, M.L. / Siebenhaar, S. / Jansen, T. / Meier, E.P.W. / Jenkins, T.P. / Bjorn, S.P. / Nguyen, G.T.T. / Lomonte, B. / Gutierrez, J.M. / Sorensen, C. ...

History

Deposition	Jan 7, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hxo.cif.gz	453 KB	Display	PDBx/mmCIF format
PDB format	pdb9hxo.ent.gz	307.3 KB	Display	PDB format
PDBx/mmJSON format	9hxo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hxo_validation.pdf.gz	511 KB	Display	wwPDB validaton report
Full document	9hxo_full_validation.pdf.gz	518.3 KB	Display
Data in XML	9hxo_validation.xml.gz	38.6 KB	Display
Data in CIF	9hxo_validation.cif.gz	52.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/9hxo ftp://data.pdbj.org/pub/pdb/validation_reports/hx/9hxo	HTTPS FTP

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Related structure data

Related structure data	9fysC 9fytC 9hubC 9huoC 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	#71 - Nov 2005 Acetylcholine Receptor similarity (4) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #54 - Jun 2004 Acetylcholinesterase similarity (3)

Deposited unit

A: Alpha-cobratoxin

B: Alpha-cobratoxin

I: light chain

M: heavy chain

C: light chain

D: heavy chain

hetero molecules

71.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alpha-cobratoxin

hetero molecules

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

2

B: Alpha-cobratoxin

hetero molecules

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

3

I: light chain

M: heavy chain

hetero molecules

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

4

C: light chain

D: heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.947, 82.653, 98.190
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 2 molecules AB

#1: Protein	Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3 Mass: 7842.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: alpha cobratoxin / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01391

#1: Protein

Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...

Mass: 7842.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: alpha cobratoxin / Source: (natural)

Naja kaouthia (monocled cobra) / References: UniProt: P01391

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Antibody , 2 types, 4 molecules ICMD

#2: Antibody	light chain Mass: 15073.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: light chain AO1 / Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody	heavy chain Mass: 12420.419 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: AO1 heavy chain / Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 6 types, 644 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#7: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#8: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.21 Å³/Da / Density % sol: 44.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 25% PEG3350, 0.1M Bis-Tris pH 6.0, 0.3 M Ammonium Sulphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.49→60.57 Å / Num. obs: 53424 / % possible obs: 52.03 % / Redundancy: 13.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.171 / R_pim(I) all: 0.048 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.49→1.52 Å / R_merge(I) obs: 1 / Num. unique obs: 415 / CC_1/2: 0.637 / R_pim(I) all: 0.479 / % possible all: 7.79

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5156	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.49→60.57 Å / SU ML: 0.1564 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2485	2612	4.89 %
R_work	0.2035	50811	-
obs	0.2056	53423	52.03 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.49→60.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4812	0	39	636	5487

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0052	5081
X-RAY DIFFRACTION	f_angle_d	0.7118	6924
X-RAY DIFFRACTION	f_chiral_restr	0.0713	747
X-RAY DIFFRACTION	f_plane_restr	0.0065	907
X-RAY DIFFRACTION	f_dihedral_angle_d	14.874	1825

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 (%)
1.49-1.52	0.2434	23	0.2997	392	X-RAY DIFFRACTION	7.79
1.52-1.55	0.4069	28	0.2928	612	X-RAY DIFFRACTION	11.95
1.55-1.58	0.3473	43	0.2864	823	X-RAY DIFFRACTION	16.24
1.58-1.61	0.3605	61	0.2885	986	X-RAY DIFFRACTION	19.61
1.61-1.65	0.3072	56	0.2824	1156	X-RAY DIFFRACTION	22.8
1.65-1.69	0.2864	83	0.2776	1299	X-RAY DIFFRACTION	25.71
1.69-1.74	0.3012	90	0.2769	1482	X-RAY DIFFRACTION	29.36
1.74-1.79	0.303	105	0.2685	1745	X-RAY DIFFRACTION	34.48
1.79-1.85	0.2793	115	0.2535	2044	X-RAY DIFFRACTION	40.26
1.85-1.91	0.2981	113	0.2548	2423	X-RAY DIFFRACTION	47.38
1.91-1.99	0.2622	144	0.2377	2755	X-RAY DIFFRACTION	53.9
1.99-2.08	0.284	152	0.2334	3070	X-RAY DIFFRACTION	59.58
2.08-2.19	0.2546	161	0.2208	3302	X-RAY DIFFRACTION	64.52
2.19-2.33	0.3121	206	0.229	3797	X-RAY DIFFRACTION	73.86
2.33-2.5	0.2585	207	0.2246	4194	X-RAY DIFFRACTION	81.05
2.5-2.76	0.2697	225	0.2191	4936	X-RAY DIFFRACTION	94.73
2.76-3.16	0.2368	235	0.2038	5193	X-RAY DIFFRACTION	99.76
3.16-3.98	0.2212	249	0.1721	5263	X-RAY DIFFRACTION	99.76
3.98-60.57	0.2136	316	0.161	5339	X-RAY DIFFRACTION	98.62

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	1.08501172441	0.395358996661	-0.0705440675928	1.03098655373	-0.221194230851	1.11964788555	0.228129343947	-0.0679350752145	0.306211626714	0.266909646092	-0.0604298663772	0.374753090021	-0.431606487084	-0.0457134746275	-0.073998005032	0.226302065843	-0.0236360600412	0.0999570070902	0.112904187821	-0.0791440194293	0.0991434738934	1.54406605138	11.3883002499	18.733889585
2	3.14527886994	-0.0583264778032	-0.328972700487	2.10076974918	2.92564283875	5.56779820544	0.0756003458366	0.27387296217	0.231018852232	-0.147289640035	0.057616099211	0.319910132011	-0.906623909844	-0.204301955379	0.116845720561	0.276074832009	0.130786003565	0.110531694224	0.1184372251	0.0931330802932	0.400367971136	-6.84226533031	17.1390071492	16.1887218675
3	3.03561955724	0.496122871652	-0.136258075584	2.28931189924	-1.68795477439	1.37044401939	-0.00323632053611	0.32533078167	-0.115283517224	-0.027808632269	0.0587505209771	0.11681368186	0.0781797846898	-0.280950397893	-0.00952551537372	0.120605447651	-0.0170127615969	0.043654879149	0.0232176009626	-0.00873517146506	0.12670593967	-1.81048841343	2.4849330973	16.9204905606
4	0.802087367284	-0.254024722546	0.126511771428	0.937696216395	0.437052847458	1.77290738846	-0.0763834416374	0.317384367413	0.20732167865	-0.14468091919	0.0511440294332	0.0679356745533	-0.203725747869	0.159203810076	-0.0303072375886	0.125939023732	-0.0386228124808	-0.0257071817118	0.192974950789	0.0583400541928	0.0651771672986	-1.46482378401	11.9671777643	-16.3322835259
5	2.75040211939	-0.751712844649	-0.933019702741	0.874891908919	0.575417151583	7.75637611148	0.138620610161	-0.352458141305	0.169339131904	0.398006638339	0.0182098658838	-0.273670717849	-0.399084409491	0.0702548417151	-0.175327836325	0.281121700064	-0.131841602467	0.0251766256748	0.252382732772	-0.0168762178855	0.161372456388	7.2386550415	17.6488633438	-13.8665532091
6	2.65711894811	-0.149506070721	-0.744102556417	1.81788664329	0.429574922229	4.0694268596	-0.179728219504	-0.100172091417	-0.271594988899	0.127561083744	-0.0786982916619	0.00168787411102	0.04917908692	0.313750118649	0.247695282352	0.0981752080721	0.00195321922829	0.00640082609306	0.200729995847	-0.00840859107945	0.0976266393384	1.9494487191	3.04420119442	-15.1792147292
7	2.23243939229	-0.182199667927	0.197829185915	1.28143822928	0.358392143265	2.42325574834	0.0892314416437	0.298280585545	0.026366576861	-0.320156652345	-0.117950492704	0.0530620469953	-0.155986881745	-0.0768430721792	0.00184560978813	0.0485629237871	0.014417537355	-0.0155740050862	0.0787133065871	0.0726794093613	0.0449479285767	-31.7685039803	-5.72967813733	-9.87814492614
8	0.437876156256	0.846408063339	0.515690378808	2.67378477811	0.439704061133	0.901335544807	-0.240940786425	0.724550548332	0.633426250376	-0.771113076308	0.0150640501467	0.575359048042	-0.781132466511	-0.586758523286	0.0700865306417	0.277047771057	0.063545361589	-0.0928922840431	0.385363819371	0.121320702881	0.226134928409	-20.0264144788	8.10462412757	-11.2302870726
9	2.7002226077	0.546698443436	0.129255148839	1.6924178843	0.57679665412	1.02306345074	0.0620018979138	0.170244326398	-0.0915744028165	-0.0290445399403	0.0390151677409	-0.0492905118031	-0.00863570693588	0.0340259935059	-0.08333845745	0.067419049536	0.030136028397	-0.0137209978151	0.0862562659652	-0.00236330502976	0.0604080088745	-22.116955818	-9.01491235302	-6.54382088174
10	3.64157879976	1.91157041027	-0.636844222714	1.26437981054	-0.383876449686	0.741898304179	0.0300304828804	-0.0701000154044	0.0988097981002	0.00702931378416	-0.017968878346	0.0760257755425	-0.0193930742569	0.0576478976773	-0.0248282979751	0.0951163018921	0.003357897387	-0.0052646141974	0.0660246343159	0.0100793762546	0.0721385493386	-20.9525861898	0.521976867796	-3.77302400687
11	5.1354832101	0.736746812234	2.71041603421	4.27820907723	-0.930350247378	1.84914988061	-0.211524763892	0.398508254429	-0.482146675029	-0.593131385524	-0.00496000794398	-0.475969010106	0.291691212609	0.345963074408	0.167495992544	0.256214450373	0.0320558450038	0.0557927763701	0.0840392461089	0.0228585102568	0.194993772345	-16.1832257365	-9.13257553632	13.2527351559
12	1.77872204646	-0.0475253693921	-0.580047481457	0.886089892895	0.263676303909	1.80779327257	0.0334570607883	-0.130893060329	0.063499554789	0.00390228694804	-0.00103848896697	-0.0890607278015	-0.00917518602144	0.133712154568	-0.0320580718263	0.0495372710168	-0.00109900953178	0.00471230503151	0.0353627912046	0.0120741265774	0.0452264166207	-22.567745471	2.40743447268	15.6859210376
13	3.46008500816	1.28608238267	0.480519429482	1.28780982208	1.32799757013	2.07416541549	0.0624490212811	-0.171634794324	-0.155655466445	0.025161863763	0.075363883511	-0.618265803179	0.0634373815627	0.0642623214372	-0.0612942095354	0.0751002544056	-0.0370638123904	-0.0437379822283	0.101223243867	0.00300688689658	0.134299230626	33.0359739398	-7.09060454095	10.3557356134
14	7.96773180328	-0.127783484967	-0.38961447161	4.24205962809	0.560375905227	5.3143276773	0.213247719366	-0.51409754952	0.277520570073	0.546088497005	-0.0257205372097	-0.27960638958	-0.579865102725	-0.159032640243	-0.143282460878	0.193728584947	0.0292911684144	-0.0173634912114	0.185736743512	-0.0421893258043	0.0975689448777	29.2492111664	-2.72016919582	13.8719495193
15	0.552567572585	-0.604033066783	-0.414271511348	0.674122398064	0.738930368118	6.95822194643	0.0742721765975	-1.4226932539	0.840243623913	1.21849640227	-0.0425916196588	-1.48634968517	-0.932489735207	1.00719881363	0.00192700912735	0.333784594867	-0.101426925702	-0.147702732272	0.410022936093	-0.0819605859982	0.380364310663	19.386065669	6.94161461061	13.3286042961
16	3.03597462069	0.108927117653	0.27805049456	1.45354029797	-0.980698592403	1.54558829742	0.19315411059	-0.133674814426	-0.131260250394	0.0857968504996	0.00168654489843	0.0704431368413	-0.00316231337014	-0.0673486593063	-0.143077514741	0.101044020872	-0.0438300461482	-0.0148346111856	0.0951028119294	-0.000994530269125	0.110415963026	22.4636788764	-8.79952401895	8.33834169684
17	3.94032437815	-1.78459294745	-0.779623709861	1.07082823611	0.367865793221	1.02215736023	0.0944242412574	-0.0391275752794	-0.0637135142081	-0.0475909170665	-0.0264369163462	-0.0322237880208	-0.0966109077389	-0.00353318847319	-0.0662735026841	0.0926791918345	-0.0240197079789	0.00215724865332	0.0812309807497	-0.0129530908482	0.0974462683679	20.7628137611	0.665942946337	5.48416825207
18	6.64774041044	-0.812309527663	-1.95735885389	3.82682617478	0.918329695634	4.0208606257	0.14069941902	-0.175445197271	-0.611225574184	0.0711123755104	-0.320430955618	0.402730665181	0.539356597847	-0.484835972896	0.305233663044	0.134800792371	-0.0312959758279	-0.00691206714559	0.243318830163	-0.0439884292434	0.17086930913	16.2652931912	-8.55933400045	-11.9814085021
19	1.49798183152	-0.0425396819791	-0.315099036372	0.66439249901	0.295721440246	1.74834135004	0.0271987349235	0.235818320682	0.144512927492	-0.107949868202	0.0155552350014	-0.0170271487906	-0.143579443618	-0.0135376804196	-0.0542299809937	0.101103607138	-0.00032143101542	0.0116815620357	0.0801033851457	-0.00319252904492	0.0842949441297	22.3928059417	2.96209135912	-13.7337402864

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 1 through 42 )	A	A	1 - 42	1 - 42
2	2	chain 'A' and (resid 43 through 57 )	A	A	43 - 57	43 - 57
3	3	chain 'A' and (resid 58 through 71 )	A	A	58 - 71	58 - 71
4	4	chain 'B' and (resid 1 through 42 )	B	B	1 - 42	1 - 42
5	5	chain 'B' and (resid 43 through 57 )	B	B	43 - 57	43 - 57
6	6	chain 'B' and (resid 58 through 71 )	B	B	58 - 71	58 - 71
7	7	chain 'I' and (resid 1 through 24 )	I	E	1 - 24	1 - 24
8	8	chain 'I' and (resid 25 through 33 )	I	E	25 - 33	25 - 33
9	9	chain 'I' and (resid 34 through 87 )	I	E	34 - 87	34 - 91
10	10	chain 'I' and (resid 88 through 113 )	I	E	88 - 113	92 - 131
11	11	chain 'M' and (resid 0 through 8 )	M	F	0 - 8	1 - 9
12	12	chain 'M' and (resid 9 through 1006 )	M	F	9 - 1006	10 - 115
13	13	chain 'C' and (resid 1 through 17 )	C	K	1 - 17	1 - 17
14	14	chain 'C' and (resid 18 through 25 )	C	K	18 - 25	18 - 25
15	15	chain 'C' and (resid 26 through 33 )	C	K	26 - 33	26 - 33
16	16	chain 'C' and (resid 34 through 87 )	C	K	34 - 87	34 - 91
17	17	chain 'C' and (resid 88 through 113 )	C	K	88 - 113	92 - 131
18	18	chain 'D' and (resid 0 through 8 )	D	L	0 - 8	1 - 9
19	19	chain 'D' and (resid 9 through 1006 )	D	L	9 - 1006	10 - 115

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