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- PDB-1t37: Design of specific inhibitors of phospholipase A2: Crystal struct... -

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Basic information

Entry
Database: PDB / ID: 1t37
TitleDesign of specific inhibitors of phospholipase A2: Crystal structure of the complex formed between group I phospholipase A2 and a designed pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.6A resolution
Components
  • Phospholipase A2 isoform 3
  • Synthetic peptidePeptide synthesis
KeywordsHYDROLASE / Phospholipase A2 / complex / Inhibition
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...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 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSingh, R.K. / Singh, N. / Jabeen, T. / Makker, J. / Sharma, S. / Dey, S. / Singh, T.P.
CitationJournal: J.Drug Target. / Year: 2005
Title: Crystal structure of the complex of group I PLA2 with a group II-specific peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) at 2.6 A resolution.
Authors: Singh, R.K. / Singh, N. / Jabeen, T. / Sharma, S. / Dey, S. / Singh, T.P.
History
DepositionApr 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 isoform 3
P: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9155
Polymers13,7382
Non-polymers1773
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.624, 42.624, 65.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Phospholipase A2 isoform 3 / Phosphatidylcholine 2-acylhydrolase


Mass: 13172.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: Venom / References: UniProt: P60045, phospholipase A2
#2: Protein/peptide Synthetic peptide / Peptide synthesis


Mass: 565.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.1 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10mM Sodium phosphate buffer, 35% Ethanol, 2mM Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 4, 2003 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 3626 / Num. obs: 3626 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 47.7 Å2 / Rsym value: 0.108 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.65 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.352 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFF

1lff
PDB Unreleased entry


Resolution: 2.6→19.36 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 721920.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 176 5.3 %RANDOM
Rwork0.191 ---
all0.256 3626 --
obs0.191 3306 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 90.3398 Å2 / ksol: 0.398971 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 12 55 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_mcangle_it4.022
X-RAY DIFFRACTIONc_scbond_it5.282
X-RAY DIFFRACTIONc_scangle_it6.952.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 27 6.3 %
Rwork0.256 399 -
obs--70.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMACY.TOP
X-RAY DIFFRACTION4ACY.PARION.TOP

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