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- PDB-5v8r: Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxi... -

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Basic information

Entry
Database: PDB / ID: 5v8r
TitleSmall Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain
ComponentsBotulinum neurotoxin type A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metalloprotease / drug design / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-90J / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAllen, K.N. / Silvaggi, N.R.
CitationJournal: Toxicon / Year: 2017
Title: Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A.
Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / ...Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / Malizio, C.J. / Johnson, E.A. / Pellett, S. / Tepp, W.H. / Tzipori, S.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2686
Polymers101,6352
Non-polymers6334
Water6,215345
1
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1343
Polymers50,8171
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1343
Polymers50,8171
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.534, 67.635, 98.112
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 50817.273 Da / Num. of mol.: 2 / Fragment: residues 1-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-90J / N-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]-2-sulfanylacetamide


Mass: 251.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H10FN3OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Mix equal volumes of 10 mg/ml enzyme (20 mM HEPES, pH 7.5, 50 mM NaCl) with crystallization solution (10%-15% polyethylene glycol monomethyl ether 2000, 0.3 M (NH4)2HPO4, 50 mM Tris, pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2008
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 69817 / % possible obs: 94.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5553 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 1.9→29.484 Å / SU ML: 1 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.222 3389 5 %
Rwork0.1746 --
obs0.1769 67754 92.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 55.85 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6557 0 0 345 6902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166764
X-RAY DIFFRACTIONf_angle_d1.4449146
X-RAY DIFFRACTIONf_dihedral_angle_d19.032464
X-RAY DIFFRACTIONf_chiral_restr0.102993
X-RAY DIFFRACTIONf_plane_restr0.0071179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92710.2308920.20881622X-RAY DIFFRACTION56
1.9271-1.95590.27951060.21442162X-RAY DIFFRACTION75
1.9559-1.98650.23711230.20422391X-RAY DIFFRACTION82
1.9865-2.0190.25781340.19712454X-RAY DIFFRACTION86
2.019-2.05380.2631360.18642596X-RAY DIFFRACTION89
2.0538-2.09120.24571330.17782631X-RAY DIFFRACTION90
2.0912-2.13140.2451420.17922659X-RAY DIFFRACTION93
2.1314-2.17490.2361410.16822724X-RAY DIFFRACTION94
2.1749-2.22210.22091460.1712730X-RAY DIFFRACTION95
2.2221-2.27380.2291470.16992771X-RAY DIFFRACTION96
2.2738-2.33070.25781470.17552761X-RAY DIFFRACTION95
2.3307-2.39360.23711480.16782791X-RAY DIFFRACTION97
2.3936-2.4640.24761470.17712802X-RAY DIFFRACTION97
2.464-2.54350.23961480.17422804X-RAY DIFFRACTION97
2.5435-2.63440.21421490.16672830X-RAY DIFFRACTION97
2.6344-2.73980.24291500.17262821X-RAY DIFFRACTION97
2.7398-2.86440.26011500.18442830X-RAY DIFFRACTION98
2.8644-3.01530.21211480.18852875X-RAY DIFFRACTION99
3.0153-3.2040.24061530.18772889X-RAY DIFFRACTION99
3.204-3.4510.23691500.17672854X-RAY DIFFRACTION99
3.451-3.79760.21541520.16772894X-RAY DIFFRACTION98
3.7976-4.34570.18771490.15152833X-RAY DIFFRACTION97
4.3457-5.46940.18451500.14542842X-RAY DIFFRACTION96
5.4694-29.4880.2011480.19352799X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -16.492 Å / Origin y: -21.3345 Å / Origin z: -22.2337 Å
111213212223313233
T0.211 Å2-0.0205 Å2-0.0742 Å2-0.0577 Å20.0121 Å2--0.113 Å2
L0.5254 °20.0214 °20.1712 °2-1.1152 °20.1359 °2--0.6365 °2
S0.0506 Å °0.002 Å °-0.0368 Å °-0.0448 Å °-0.0442 Å °0.0122 Å °0.0037 Å °-0.0549 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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