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- PDB-2fnx: Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2):... -

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Basic information

Entry
Database: PDB / ID: 2fnx
TitleDesign of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution
Components
  • Inhibitor peptide
  • Phospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE / peptide inhibitor complex
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
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, 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, N. / Srivastava, P. / Sharma, S. / Dey, S. / Singh, T.P.
CitationJournal: To be Published
Title: Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution
Authors: Singh, N. / Srivastava, P. / Sharma, S. / Dey, S. / Singh, T.P.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
P: Inhibitor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1563
Polymers14,0602
Non-polymers961
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-15 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.060, 53.060, 48.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa / Phosphatidylcholine 2- acylhydrolase / DPLA2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Protein/peptide Inhibitor peptide


Mass: 430.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized peptide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M ammonoium sulfate, 30% PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→52.7 Å / Num. all: 3181 / Num. obs: 3181 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.73 Å / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→52.7 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.465 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23098 332 9.5 %RANDOM
Rwork0.18938 ---
all0.221 3181 --
obs0.19337 3181 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 5 57 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021997
X-RAY DIFFRACTIONr_angle_refined_deg2.5631.9971329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8813116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40215187
X-RAY DIFFRACTIONr_chiral_restr0.110.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02717
X-RAY DIFFRACTIONr_nbd_refined0.4110.3498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.579
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.313
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.54
X-RAY DIFFRACTIONr_mcbond_it1.1291.5612
X-RAY DIFFRACTIONr_mcangle_it2.2462965
X-RAY DIFFRACTIONr_scbond_it2.8753385
X-RAY DIFFRACTIONr_scangle_it5.0854.5364
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 19
Rwork0.249 240

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