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- PDB-2abx: THE CRYSTAL STRUCTURE OF ALPHA-BUNGAROTOXIN AT 2.5 ANGSTROMS RESO... -

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Basic information

Entry
Database: PDB / ID: 2abx
TitleTHE CRYSTAL STRUCTURE OF ALPHA-BUNGAROTOXIN AT 2.5 ANGSTROMS RESOLUTION. RELATION TO SOLUTION STRUCTURE AND BINDING TO ACETYLCHOLINE RECEPTOR
ComponentsALPHA-BUNGAROTOXIN
KeywordsPOSTSYNAPTIC NEUROTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesBungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLove, R. / Stroud, R.
Citation
Journal: Protein Eng. / Year: 1986
Title: The crystal structure of alpha-bungarotoxin at 2.5 A resolution: relation to solution structure and binding to acetylcholine receptor.
Authors: Love, R.A. / Stroud, R.M.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1982
Title: Alpha-Bungarotoxin Structure Revealed by a Rapid Method for Averaging Electron Density of Non-Crystallographically Translationally Related Molecules
Authors: Agard, D.A. / Stroud, R.M.
History
DepositionFeb 19, 1986Processing site: BNL
SupersessionMay 7, 1986ID: 1ABX
Revision 1.0May 7, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN
B: ALPHA-BUNGAROTOXIN


Theoretical massNumber of molelcules
Total (without water)16,0112
Polymers16,0112
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.800, 78.400, 22.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (-1), (1) / Vector: 72.1, 105.95)

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Components

#1: Protein ALPHA-BUNGAROTOXIN


Mass: 8005.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Tissue: VENOM / References: UniProt: P60615
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal grow
*PLUS
Temperature: 4-20 ℃ / Method: unknown / PH range low: 9 / PH range high: 7

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. all: 4511 / Num. obs: 3968 / % possible obs: 77 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.24 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 16 1118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.032
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg5.8
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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