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- PDB-4gfy: Design of peptide inhibitors of phospholipase A2: crystal Structu... -

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Basic information

Entry
Database: PDB / ID: 4gfy
TitleDesign of peptide inhibitors of phospholipase A2: crystal Structure of phospholipase A2 complexed with a designed tetrapeptide Val - Ilu- Ala - Lys at 2.7 A resolution
Components
  • Phospholipase A2 VRV-PL-VIIIa
  • VIAK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PLA2 / ANTI-INFLAMMATORY / ANTI-COAGULANT / PEPTIDE-INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid 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 / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShukla, P.K. / Sinha, M. / Dey, S. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Design of peptide inhibitors of phospholipase A2: crystal Structure of phospholipase A2 complexed with a designed tetrapeptide Val - Ilu- Ala - Lys at 2.7 A resolution
Authors: Shukla, P.K. / Sinha, M. / Dey, S. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionAug 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
B: VIAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1563
Polymers14,0602
Non-polymers961
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-15 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.035, 53.035, 48.469
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 / PlA2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake)
References: UniProt: D0VX11, UniProt: P59071*PLUS, phospholipase A2
#2: Protein/peptide VIAK


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


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


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.3M AMMONIUM SULPHATE, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 2005 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→53.2 Å / Num. obs: 3875 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.138 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.73 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.458 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FGA

4fga


Resolution: 2.7→53.03 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.795 / SU B: 12.626 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24785 136 4.5 %RANDOM
Rwork0.22592 ---
all0.22694 ---
obs0.22694 2892 80.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→53.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 5 48 1027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_angle_refined_deg2.555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.563
X-RAY DIFFRACTIONr_chiral_restr0.102
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_mcbond_it1.497
X-RAY DIFFRACTIONr_mcangle_it2.718
X-RAY DIFFRACTIONr_scbond_it
LS refinement shellResolution: 2.703→2.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 11 -
Rwork0.317 209 -
obs--76.39 %

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