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- PDB-4fga: Design of peptide inhibitors of group II phospholipase A2: Crysta... -

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Basic information

Entry
Database: PDB / ID: 4fga
TitleDesign of peptide inhibitors of group II phospholipase A2: Crystal structure of the complex of phospholipsae A2 with a designed tripeptide, Ala- Tyr- Lys at 2.3 A resolution
Components
  • AYK
  • Phospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PLA2 / Anti-inflammatory / Anti-coagulant / Peptide-inhibitor / Hydrolase / 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: 2.3 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 group II phospholipase A2: Crystal structure of the complex of phospholipsae A2 with a designed tripeptide, Ala- Tyr- Lys at 2.3 A resolution
Authors: Shukla, P.K. / Sinha, M. / Dey, S. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
P: AYK


Theoretical massNumber of molelcules
Total (without water)14,0112
Polymers14,0112
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-3 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.166, 53.166, 48.548
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


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 AYK


Mass: 381.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
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: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 2006 / 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: 2.3→53.17 Å / Num. obs: 5887 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.116 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIX

4eix


Resolution: 2.3→53.17 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.781 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.413 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24342 275 4.6 %RANDOM
Rwork0.20039 ---
all0.20246 ---
obs0.20246 5723 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 98 1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02995
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9891328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48423.8142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56715179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.259155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021721
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 20 -
Rwork0.274 390 -
obs--100 %

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