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- PDB-1bun: STRUCTURE OF BETA2-BUNGAROTOXIN: POTASSIUM CHANNEL BINDING BY KUN... -

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Basic information

Entry
Database: PDB / ID: 1bun
TitleSTRUCTURE OF BETA2-BUNGAROTOXIN: POTASSIUM CHANNEL BINDING BY KUNITZ MODULES AND TARGETED PHOSPHOLIPASE ACTION
Components(BETA2-BUNGAROTOXIN) x 2
KeywordsTOXIN / HYDROLASE / PRESYNAPTIC NEUROTOXIN
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / potassium channel regulator activity / phospholipid metabolic process / lipid catabolic process / serine-type endopeptidase inhibitor activity / phospholipid binding / toxin activity / calcium ion binding ...phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / potassium channel regulator activity / phospholipid metabolic process / lipid catabolic process / serine-type endopeptidase inhibitor activity / phospholipid binding / toxin activity / calcium ion binding / extracellular space / extracellular region
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 beta-bungarotoxin A1 chain / Kunitz-type serine protease inhibitor homolog beta-bungarotoxin B2 chain
Similarity search - Component
Biological speciesBungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsKwong, P.D. / Mcdonald, N.Q. / Sigler, P.B. / Hendrickson, W.A.
CitationJournal: Structure / Year: 1995
Title: Structure of beta 2-bungarotoxin: potassium channel binding by Kunitz modules and targeted phospholipase action.
Authors: Kwong, P.D. / McDonald, N.Q. / Sigler, P.B. / Hendrickson, W.A.
History
DepositionOct 15, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA2-BUNGAROTOXIN
B: BETA2-BUNGAROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7814
Polymers20,7352
Non-polymers462
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-28 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 52.600, 177.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-129-

HOH

21B-71-

HOH

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Components

#1: Protein BETA2-BUNGAROTOXIN / PHOSPHATIDE ACYL-HYDROLASE / PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE


Mass: 13521.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NUMEROUS NATURAL ISOFORMS, THIS IS THE BETA2 ISOFORM
Source: (natural) Bungarus multicinctus (many-banded krait) / Tissue: VENOM / References: UniProt: P00617, phospholipase A2
#2: Protein BETA2-BUNGAROTOXIN / PHOSPHATIDE ACYL-HYDROLASE / PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE


Mass: 7213.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NUMEROUS NATURAL ISOFORMS, THIS IS THE BETA2 ISOFORM
Source: (natural) Bungarus multicinctus (many-banded krait) / Tissue: VENOM / References: UniProt: P00989, phospholipase A2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE NUMBERING IS 1 - 120 (A) FOR THE PHOSPHOLIPASE 1 - 61 (B) FOR THE KUNITZ MODULE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.5 mMEDTA1drop
30.01 %1dropNaN3
41.4 M1dropNaCl
53.3 M1reservoirNaCl
650 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.54
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→10 Å / Num. obs: 9372 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.25 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Num. measured all: 30515 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.45→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.281 -10 %
Rwork0.193 --
obs0.193 7817 -
Refinement stepCycle: LAST / Resolution: 2.45→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 2 81 1523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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