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- PDB-8dnd: Crystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and sy... -

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Basic information

Entry
Database: PDB / ID: 8dnd
TitleCrystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and synthetic inhibitor Varespladib (LY315920)
ComponentsBasic phospholipase A2 homolog piratoxin-1
KeywordsTOXIN/ANTITOXIN / PrTX-I / varespladib / Bothrops pirajai / PLA2-like toxin / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


A2-type glycerophospholipase activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily
Similarity search - Domain/homology
Chem-VRD / Basic phospholipase A2 homolog piratoxin-1
Similarity search - Component
Biological speciesBothrops pirajai (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.018 Å
AuthorsSalvador, G.H.M. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/10143-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Biochimie / Year: 2023
Title: Structural basis of the myotoxic inhibition of the Bothrops pirajai PrTX-I by the synthetic varespladib.
Authors: Salvador, G.H.M. / Pinto, E.K.R. / Ortolani, P.L. / Fortes-Dias, C.L. / Cavalcante, W.L.G. / Soares, A.M. / Lomonte, B. / Lewin, M.R. / Fontes, M.R.M.
History
DepositionJul 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Mar 4, 2026Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Basic phospholipase A2 homolog piratoxin-1
A: Basic phospholipase A2 homolog piratoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0349
Polymers27,5082
Non-polymers1,5257
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-64 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.748, 72.660, 44.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-323-

HOH

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Components

#1: Protein Basic phospholipase A2 homolog piratoxin-1 / svPLA2 homolog / Myotoxin SIV-SP5 / Piratoxin-I / PrTX-I


Mass: 13754.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops pirajai (snake) / Tissue: venom gland / References: UniProt: P58399
#2: Chemical ChemComp-VRD / ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid / Varespladib


Mass: 380.394 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H20N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% w/v PEG 4000, 0.1 M Tris HCl pH 8.5 and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.018→50.32 Å / Num. obs: 15085 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.02-2.136.30.6641375921880.8260.2860.7242.6100
6.38-50.325.90.04733135570.9990.0210.0523099.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.7 Å50.32 Å
Translation3.7 Å50.32 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q2j

2q2j


Resolution: 2.018→50.317 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 823 5.47 %
Rwork0.1916 14227 -
obs0.193 15050 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.48 Å2 / Biso mean: 31.0594 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 2.018→50.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 104 165 2135
Biso mean--46.71 34.86 -
Num. residues----242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.018-2.14440.27461250.23882355100
2.1444-2.310.26861200.2228209688
2.31-2.54240.25881510.20842376100
2.5424-2.91030.21981540.20782402100
2.9103-3.66650.19091250.17782443100
3.6665-50.3170.19441480.17112555100
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)
11.18620.3488-0.35277.47722.86943.3677-0.0836-0.02880.17610.01220.02780.6308-0.126-0.21840.0560.1502-0.00880.01180.20840.02280.2036-29.21896.6474-15.5947
26.6859-0.34882.98053.29981.9538.0390.1304-0.0895-0.54680.7150.32840.00580.31030.0638-0.38620.25280.00570.02090.19640.0150.2036-24.0116-1.6071-12.8334
33.25360.66010.17045.19171.11232.85060.1533-0.45560.47320.42230.0431-0.97090.07430.8987-0.18650.24810.0083-0.04930.4204-0.08490.4144-11.32444.1519-16.2247
43.1606-2.3174-0.16288.0741-0.52272.6803-0.12160.07080.29750.05830.1483-0.6671-0.14420.4175-0.00110.1782-0.02480.00360.2159-0.02250.2704-15.36139.7187-21.3608
53.43572.1941-1.08065.2834-0.83831.40680.0279-0.15810.56250.0533-0.02660.7589-0.4188-0.16220.01130.23360.02490.0250.1977-0.0170.3056-30.352514.045-18.4862
60.6361-1.3724-0.50384.5424-0.05791.22830.2031-0.48081.3402-0.0197-0.36350.2953-0.35910.11760.29450.21750.03510.01210.2684-0.03330.5719-33.229319.8173-22.2658
71.5253-0.2992-0.20842.6356-0.0471.28270.07340.09030.2178-0.2636-0.1093-0.1693-0.1848-0.1055-0.01580.1631-0.01540.02770.1587-0.00720.2148-25.476411.5593-23.0764
87.034-0.49891.49793.924-0.59525.8655-0.0147-0.3417-0.1710.4082-0.178-0.40710.67070.42580.15480.31570.0129-0.02420.2088-0.0190.1862-16.3518-6.161-19.695
92.07560.3122-0.54967.50362.65151.148-0.2036-0.4690.42740.50970.4169-1.06830.10020.08260.0030.59940.2527-0.07370.79010.13680.5206-9-1.1073-10.4839
103.5948-0.333-0.15992.0594-0.12383.08530.1043-0.1808-0.28970.0452-0.2253-0.5873-0.38910.80780.25250.2505-0.0423-0.07350.5323-0.07820.6569-4.700410.6648-21.1291
113.17120.44980.18912.36530.50842.4297-0.11380.22110.0774-0.1529-0.0309-0.0201-0.14740.1670.10080.2276-0.0073-0.02660.20760.01340.1894-16.2557.36362.8167
123.74380.21091.0261.5693-1.13893.2452-0.70030.71140.6064-0.21880.2069-0.0159-0.97120.34770.14180.6804-0.2018-0.22850.45210.19350.4772-8.471620.3405-1.8621
132.56491.994-0.2635.1643-0.73831.9761-0.34090.18420.0206-0.13630.2456-0.3806-0.12630.50360.10450.2042-0.0283-0.02170.27690.00160.196-5.068510.89917.2616
144.92761.38130.48471.0931-0.93332.99630.02720.13610.1008-0.2497-0.07460.40290.1119-0.2030.10880.2001-0.01230.0110.1657-0.02240.1258-26.84484.06442.7232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )B1 - 13
2X-RAY DIFFRACTION2chain 'B' and (resid 15 through 22 )B15 - 22
3X-RAY DIFFRACTION3chain 'B' and (resid 23 through 39 )B23 - 39
4X-RAY DIFFRACTION4chain 'B' and (resid 40 through 57 )B40 - 57
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 82 )B58 - 82
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 88 )B83 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 108 )B90 - 108
8X-RAY DIFFRACTION8chain 'B' and (resid 109 through 117 )B109 - 117
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 125 )B118 - 125
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 133 )B126 - 133
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 57 )A1 - 57
12X-RAY DIFFRACTION12chain 'A' and (resid 58 through 74 )A58 - 74
13X-RAY DIFFRACTION13chain 'A' and (resid 75 through 112 )A75 - 112
14X-RAY DIFFRACTION14chain 'A' and (resid 113 through 133 )A113 - 133

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