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- PDB-2ctx: THE REFINED CRYSTAL STRUCTURE OF ALPHA-COBRATOXIN FROM NAJA NAJA ... -

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Basic information

Entry
Database: PDB / ID: 2ctx
TitleTHE REFINED CRYSTAL STRUCTURE OF ALPHA-COBRATOXIN FROM NAJA NAJA SIAMENSIS AT 2.4-ANGSTROMS RESOLUTION
ComponentsALPHA-COBRATOXIN
KeywordsNEUROTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja naja (Indian cobra)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsBetzel, C. / Lange, G. / Pal, G.P. / Wilson, K.S. / Maelicke, A. / Saenger, W.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: The refined crystal structure of alpha-cobratoxin from Naja naja siamensis at 2.4-A resolution.
Authors: Betzel, C. / Lange, G. / Pal, G.P. / Wilson, K.S. / Maelicke, A. / Saenger, W.
History
DepositionSep 24, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-COBRATOXIN


Theoretical massNumber of molelcules
Total (without water)7,8421
Polymers7,8421
Non-polymers00
Water55831
1
A: ALPHA-COBRATOXIN

A: ALPHA-COBRATOXIN


Theoretical massNumber of molelcules
Total (without water)15,6842
Polymers15,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Unit cell
Length a, b, c (Å)76.610, 76.610, 42.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: RESIDUE 7 IS A CIS PROLINE.
2: THE SIDE CHAINS OF RESIDUES ILE 9, ALA 28, ARG 68, LYS 69, ARG 70, AND PRO 71 ARE HIGHLY MOBILE.
Components on special symmetry positions
IDModelComponents
11A-73-

HOH

21A-88-

HOH

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Components

#1: Protein ALPHA-COBRATOXIN


Mass: 7842.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja naja (Indian cobra) / References: UniProt: P25671
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 %(w/w)protein solution11aqueous solution
275 %MPD12
30.05 Mglycine HCl12

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 3271 / Num. measured all: 12612 / Rmerge(I) obs: 0.074

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.195 3271
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms518 0 0 31 549
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.01
X-RAY DIFFRACTIONp_angle_d0.0710.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0850.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6911
X-RAY DIFFRACTIONp_mcangle_it2.8651
X-RAY DIFFRACTIONp_scbond_it1.6731.3
X-RAY DIFFRACTIONp_scangle_it2.9041.3
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2560.1
X-RAY DIFFRACTIONp_singtor_nbd0.2470.5
X-RAY DIFFRACTIONp_multtor_nbd0.4030.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3490.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.61.3
X-RAY DIFFRACTIONp_staggered_tor26.812
X-RAY DIFFRACTIONp_orthonormal_tor23.113
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection all: 3271 / σ(F): 0 / Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.9 Å2

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