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- PDB-1skg: Structure-based rational drug design: Crystal structure of the co... -

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Basic information

Entry
Database: PDB / ID: 1skg
TitleStructure-based rational drug design: Crystal structure of the complex formed between Phospholipase A2 and a pentapeptide Val-Ala-Phe-Arg-Ser
Components
  • Phospholipase A2
  • VAFRS
KeywordsHYDROLASE / rational drug design / vafrs complex / phospholipase a2
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
METHANOL / : / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsEthayathulla, A.S. / Singh, N. / Sharma, S. / Makker, J. / Dey, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: To be Published
Title: Structure-based rational drug design: Crystal structure of the complex formed between Phospholipase A2 and a pentapeptide Val-Ala-Phe-Arg-Ser
Authors: Ethayathulla, A.S. / Singh, N. / Sharma, S. / Makker, J. / Dey, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
B: VAFRS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6588
Polymers14,2092
Non-polymers4486
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-46 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.350, 52.350, 47.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological Unit is a monomer

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Components

#1: Protein Phospholipase A2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: Venom / Species: Daboia russellii / Strain: pulchella
References: GenBank: 1839639, UniProt: P59071*PLUS, phospholipase A2
#2: Protein/peptide VAFRS


Mass: 579.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the sequence was Chemically synthesized.
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.5 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium sulphate, 30% PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.803 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 29, 2003 / Details: MIRROR
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 393280 / Num. obs: 39363 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.078 / Net I/σ(I): 16.6
Reflection shellResolution: 1.2→1.23 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.428 / % possible all: 97.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FB2

1fb2


Resolution: 1.21→20 Å / Num. parameters: 11379 / Num. restraintsaints: 13028 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 990 2.5 %RANDOM
Rwork0.141 ---
all0.1464 38357 --
obs0.1433 38357 97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 18.5 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1244.5
Refinement stepCycle: LAST / Resolution: 1.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 20 254 1258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.061
LS refinement shellResolution: 1.2→1.23 Å

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