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- PDB-6zfm: Structure of alpha-Cobratoxin with a peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 6zfm
TitleStructure of alpha-Cobratoxin with a peptide inhibitor
Components
  • Alpha-cobratoxin
  • peptide 12
KeywordsTOXIN / cobratoxin / inhibitor / three-finger toxin
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Snake toxin-like superfamily
Similarity search - Domain/homology
Chem-QJE / Alpha-cobratoxin
Similarity search - Component
Biological speciesNaja kaouthia (monocled cobra)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKiontke, S. / Kummel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU2531/2 Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: Peptide Inhibitors of the alpha-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction.
Authors: Lynagh, T. / Kiontke, S. / Meyhoff-Madsen, M. / Gless, B.H. / Johannesen, J. / Kattelmann, S. / Christiansen, A. / Dufva, M. / Laustsen, A.H. / Devkota, K. / Olsen, C.A. / Kummel, D. / Pless, S.A. / Lohse, B.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 23, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-cobratoxin
B: Alpha-cobratoxin
C: peptide 12
D: Alpha-cobratoxin
E: Alpha-cobratoxin
F: peptide 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5889
Polymers33,6716
Non-polymers9173
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-49 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.438, 49.438, 289.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12(chain C and (resid 1 through 2 or resid 4 through 9))
22(chain F and (resid 1 through 2 or resid 4 through 9))
13(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))
23(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 71
211chain DD1 - 71
112(chain C and (resid 1 through 2 or resid 4 through 9))C0
212(chain F and (resid 1 through 2 or resid 4 through 9))F0
113(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B1 - 32
123(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B34 - 35
133(chain B and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))B37 - 66
213(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E1 - 32
223(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E34 - 35
233(chain E and (resid 1 through 32 or resid 34 through 35 or resid 37 through 66))E37 - 66

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Alpha-cobratoxin / alpha-Cbtx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


Mass: 7842.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01391
#2: Protein/peptide peptide 12


Mass: 1151.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-QJE / 3-[2-[2-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propan-1-ol


Mass: 339.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H33NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Carboxylic acids (sodium formate / ammonium acetate / sodium citrate / sodium potassium tartrate / sodium oxamate), 0.1 M HEPES / MOPS pH7.5, 30.0 % v/v PEG 500 MME / PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.68→27.645 Å / Num. obs: 45445 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 34.57 Å2 / CC1/2: 0.969 / Net I/σ(I): 9.2
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 2353 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTN

1ntn


Resolution: 1.9→27.645 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1562 5 %
Rwork0.2011 29662 -
obs0.2027 31224 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.1 Å2 / Biso mean: 54.08 Å2 / Biso min: 26.19 Å2
Refinement stepCycle: final / Resolution: 1.9→27.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 16 217 2469
Biso mean--57.28 53.75 -
Num. residues----290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A720X-RAY DIFFRACTION3.779TORSIONAL
12D720X-RAY DIFFRACTION3.779TORSIONAL
21C594X-RAY DIFFRACTION3.779TORSIONAL
22F594X-RAY DIFFRACTION3.779TORSIONAL
31B68X-RAY DIFFRACTION3.779TORSIONAL
32E68X-RAY DIFFRACTION3.779TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.96130.30541390.27932660100
1.9613-2.03140.30011400.257267199
2.0314-2.11270.27581520.24792692100
2.1127-2.20880.27191730.23492647100
2.2088-2.32520.28871420.22922715100
2.3252-2.47080.30811280.22982754100
2.4708-2.66150.27031410.22612671100
2.6615-2.9290.25161220.21732721100
2.929-3.35230.21681410.21042701100
3.3523-4.22110.20021350.17252722100
4.2211-27.6450.19481490.17622708100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.4818-1.0748-2.75455.86143.23373.52780.22580.24920.0460.5877-0.05860.60960.7244-1.3307-0.22060.5348-0.0130.00070.42630.08340.38819.5202-17.734237.0018
20.3465-0.13910.02210.1160.22680.95480.17010.0516-0.3313-0.1099-0.01210.00340.59290.32420.26041.11960.4952-0.20570.45780.00640.507220.1273-25.875729.0154
37.055-0.045-0.76186.10881.17140.30580.0608-0.0758-0.3470.3413-0.093-0.27720.20351.10030.14830.32990.2135-0.06210.64340.02820.294823.6494-14.722734.8001
46.02045.48546.14955.11855.70456.3670.4155-1.950.03041.1578-0.86080.87761.1106-0.7720.49380.39160.02990.05850.76940.05260.4599-8.242-16.90249.6698
53.29865.14812.42558.03543.78551.78341.0091-1.8895-0.40942.6734-0.88330.22992.0931-0.7657-0.08660.9216-0.04340.03941.0530.14790.3678-3.7555-16.932316.5504
63.452-4.71552.88878.3091-5.77675.7730.1866-1.1063-0.29820.2912-0.19610.95820.0918-1.5242-0.01780.32020.04110.02061.0902-0.03920.4496-13.1038-12.05937.0481
75.44281.64375.35890.62311.61155.3836-0.10260.01030.20280.06750.0523-0.07340.21020.01770.11530.2180.12690.01160.39820.04860.34189.6486-12.234112.0471
83.8927-0.67394.12810.1161-0.7144.3764-0.13120.34271.19580.2698-0.304-0.2372-0.71240.18280.40580.30820.06-0.00810.46660.11310.53392.5215-7.63436.9897
93.84622.27812.26825.42444.65024.12420.14221.0434-0.7047-0.7718-0.1364-0.7676-0.79490.69630.02620.34090.03130.04760.52190.05950.32021.8577-12.60171.7102
102.2651.37552.06696.20932.63662.24210.1841-0.8061-0.41720.4869-0.6225-0.10420.8453-0.34540.39760.3795-0.0425-0.01040.60160.12230.3867-3.3777-19.67316.2255
118.8998-7.95085.03858.29-5.97364.67940.68690.1114-0.452-0.5147-0.1399-0.08111.31590.3965-0.50740.52020.1773-0.15430.43130.00950.428914.3945-18.816618.45
121.94663.05172.05226.34442.93562.7516-0.3207-0.31240.20710.25040.09471.0586-0.7525-0.84990.2670.36620.05280.10430.55240.04050.522319.0235-1.187713.2809
133.21232.8016-4.70852.5218-4.17326.9581-0.39731.03060.5282-0.8380.4151-0.3579-1.49910.69090.01730.7385-0.26880.02930.6869-0.00510.431821.61293.09365.4367
141.21280.022-0.09630.29020.14370.3240.0222-0.22330.12450.00860.1168-0.1276-0.08960.36230.12430.268-0.11690.06961.1888-0.13270.428230.7551-3.748221.3377
151.609-0.3048-0.34220.54150.26070.15180.015-0.76380.23290.21370.1719-0.3107-0.22280.7526-0.14340.3885-0.10380.17721.4076-0.24520.78535.4702-5.752911.9399
166.6851-1.29652.15366.8738-0.65390.70320.03760.2601-0.4773-0.3488-0.0433-0.24110.81840.74560.14370.3370.24760.05330.5545-0.00960.409224.5863-13.105712.1523
177.4791-4.1873-2.61583.33942.68582.41410.48640.81990.9562-1.9161-0.6549-0.0363-1.3101-0.06160.20640.69040.20760.03270.38930.04270.434910.56415.62237.2913
182.42032.82572.97863.33933.40723.790.08421.31630.8523-3.1014-0.1743-1.3238-2.52021.34940.0640.95080.07840.17690.73170.2140.783412.681311.745230.3519
194.9713-1.9373-4.8770.85112.43577.76940.23790.28580.453-1.1127-0.39650.1689-1.6564-0.79320.15340.91580.3884-0.07720.61420.01360.49183.914217.390739.9118
200.293-1.0484-1.08766.39775.42055.3418-0.18690.0453-0.10990.32990.16190.21970.15380.23750.13240.22680.10870.02820.40140.03280.309115.4501-2.231834.9526
210.3698-0.9089-0.74387.69886.29165.1414-0.0790.1952-0.123-0.4592-0.05560.6224-0.5932-0.62710.11270.29510.10090.02220.33770.06030.324510.54624.033535.4456
222.5132-4.10890.0277.01510.31820.4374-0.38430.2702-0.77680.3170.00730.82490.6085-0.44670.37890.48840.11910.21090.51050.07960.53965.5878-0.446843.9349
238.3563-5.2238-5.68423.72262.47766.766-0.2094-0.6827-0.49751.2711-0.0476-0.95240.89530.64340.26480.48030.104-0.01190.42290.05020.409311.89364.71845.2972
247.2793-4.7704-3.42235.32924.87374.7533-0.29550.19180.0819-0.6504-0.2118-0.7333-0.29410.62390.32880.5250.0420.13960.34310.07750.437315.355912.752640.7769
258.1179-4.6036-6.10446.98494.25616.16140.1265-0.35550.2129-0.24460.2716-0.7898-0.23240.9897-0.42850.28720.06990.08020.6493-0.0640.327723.4944-3.074228.5276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 57 )A19 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 71 )A58 - 71
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 5 )B1 - 5
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 11 )B6 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 18 )B12 - 18
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 35 )B19 - 35
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 52 )B36 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 57 )B53 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 66 )B58 - 66
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 9 )C2 - 9
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 10 )D1 - 10
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 18 )D11 - 18
14X-RAY DIFFRACTION14chain 'D' and (resid 19 through 42 )D19 - 42
15X-RAY DIFFRACTION15chain 'D' and (resid 43 through 57 )D43 - 57
16X-RAY DIFFRACTION16chain 'D' and (resid 58 through 71 )D58 - 71
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 5 )E1 - 5
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 11 )E6 - 11
19X-RAY DIFFRACTION19chain 'E' and (resid 12 through 18 )E12 - 18
20X-RAY DIFFRACTION20chain 'E' and (resid 19 through 35 )E19 - 35
21X-RAY DIFFRACTION21chain 'E' and (resid 36 through 42 )E36 - 42
22X-RAY DIFFRACTION22chain 'E' and (resid 43 through 52 )E43 - 52
23X-RAY DIFFRACTION23chain 'E' and (resid 53 through 57 )E53 - 57
24X-RAY DIFFRACTION24chain 'E' and (resid 58 through 66 )E58 - 66
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 9 )F2 - 9

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