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- PDB-5v8u: Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxi... -

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Basic information

Entry
Database: PDB / ID: 5v8u
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 / membrane => GO:0016020 / metalloendopeptidase activity / toxin activity ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / membrane => GO:0016020 / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / 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-90M / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)102,2966
Polymers101,6352
Non-polymers6614
Water7,350408
1
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1483
Polymers50,8171
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1483
Polymers50,8171
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.095, 67.653, 98.087
Angle α, β, γ (deg.)90.00, 105.22, 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 / Mutation: P2Q
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: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-90M / N-[3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-yl]-2-sulfanylacetamide


Mass: 265.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12FN3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Mix equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)

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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: 2.05→50 Å / Num. obs: 55823 / % possible obs: 95.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4395 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 2.05→37.563 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2000 3.58 %
Rwork0.2292 --
obs0.2303 55806 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 38 417 6731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026451
X-RAY DIFFRACTIONf_angle_d0.5658707
X-RAY DIFFRACTIONf_dihedral_angle_d13.7443816
X-RAY DIFFRACTIONf_chiral_restr0.043945
X-RAY DIFFRACTIONf_plane_restr0.0021116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.36941080.29532906X-RAY DIFFRACTION74
2.1013-2.15810.30991260.28343384X-RAY DIFFRACTION85
2.1581-2.22160.28921370.2613680X-RAY DIFFRACTION92
2.2216-2.29330.32021420.24893834X-RAY DIFFRACTION96
2.2933-2.37520.27621450.25373908X-RAY DIFFRACTION99
2.3752-2.47030.26961480.25233972X-RAY DIFFRACTION100
2.4703-2.58270.28351470.24613960X-RAY DIFFRACTION100
2.5827-2.71880.27051490.25063998X-RAY DIFFRACTION100
2.7188-2.88910.30791480.24263985X-RAY DIFFRACTION100
2.8891-3.11210.27511490.23954010X-RAY DIFFRACTION100
3.1121-3.42510.2451490.22714013X-RAY DIFFRACTION100
3.4251-3.92020.2451500.21284020X-RAY DIFFRACTION100
3.9202-4.93730.21490.18494025X-RAY DIFFRACTION100
4.9373-37.56910.26091530.22544111X-RAY DIFFRACTION100
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)
10.2864-0.25330.03630.227-0.0390.14610.0834-0.0785-0.14130.21430.0119-0.0650.07950.096700.23220.0036-0.03520.18540.0510.1727-10.626-6.1521-15.3199
20.4148-0.04730.10390.5029-0.00240.35310.0375-0.0278-0.09640.1013-0.03370.04520.0444-0.04170.00030.1289-0.0070.00980.120.02060.0943-21.920.9102-20.0824
30.0577-0.0693-0.01850.2033-0.05360.1069-0.03960.0019-0.03460.39640.22270.4646-0.1669-0.25850.3961-0.02420.14510.28980.36560.00240.3834-35.678317.6417-18.4746
40.36710.14740.34620.6366-0.36880.60160.08220.0914-0.1088-0.1099-0.03830.0953-0.006-0.0706-0.00090.13330.0038-0.00150.1454-0.00070.1575-19.01024.1651-29.4869
50.2046-0.22030.00150.2656-0.09540.1109-0.0199-0.04580.06120.0112-0.047-0.0263-0.07330.073200.1702-0.0093-0.01260.1369-0.02510.1183-2.959930.959-20.9875
60.2705-0.26380.02340.5269-0.27980.0206-0.00590.0112-0.0210.0378-0.0293-0.1616-0.05350.010400.1511-0.0193-0.01550.16390.02060.18377.463822.712-22.5793
70.03240.007-0.0250.0121-0.03940.020.05260.3110.0615-0.01810.1104-0.27020.00070.117700.2223-0.04620.0730.39750.00910.362517.962120.9277-37.6039
80.19630.0439-0.10670.14140.06770.06050.063-0.1372-0.42710.1505-0.1123-0.19490.14010.24380.01680.22830.0193-0.0260.27880.01340.340315.8595.6395-21.0551
90.58210.4225-0.02830.478-0.01970.05670.08440.1049-0.0183-0.2706-0.0957-0.09720.0491-0.0170.00740.16540.01860.0150.1589-0.02360.17763.468816.987-35.3665
100.0960.0832-0.19410.0906-0.17880.3582-0.04240.24990.1977-0.3260.07260.2890.223-0.44890.00260.31180.0151-0.02840.25460.0270.2107-9.17434.9246-46.1979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 275 )
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 299 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 416 )
5X-RAY DIFFRACTION5chain 'B' and (resid -9 through 100 )
6X-RAY DIFFRACTION6chain 'B' and (resid 101 through 232 )
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 275 )
8X-RAY DIFFRACTION8chain 'B' and (resid 276 through 321 )
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 390 )
10X-RAY DIFFRACTION10chain 'B' and (resid 391 through 416 )

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