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- PDB-1sqz: Design of specific inhibitors of Phopholipase A2: Crystal structu... -

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Basic information

Entry
Database: PDB / ID: 1sqz
TitleDesign of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution
Components
  • Phospholipase A2
  • synthetic peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PHOSPHOLIPASE A2 / DEHYDRO-IARS / TOXIN / HYDROLASE-HYDROLASE 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
DEHYDRO-ILE-ALA-ARG-SER / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii russellii (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSingh, N. / Prem Kumar, R. / Somvanshi, R.K. / Bilgrami, S. / Ethayathulla, A.S. / Sharma, S. / Dey, S. / Singh, T.P.
CitationJournal: To be Published
Title: Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between GroupII Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution
Authors: Singh, N. / Prem Kumar, R. / Somvanshi, R.K. / Bilgrami, S. / Ethayathulla, A.S. / Sharma, S. / Dey, S. / Singh, T.P.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 23, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5175
Polymers14,2292
Non-polymers2883
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-32 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.549, 52.549, 47.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological Unit is Monomer

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Components

#1: Protein Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase


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


Type: Peptide-like / Class: Inhibitor / Mass: 599.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis / References: DEHYDRO-ILE-ALA-ARG-SER
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M Ammonium sulphate,50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 29, 2003 / Details: MIRROR
RadiationMonochromator: GRAPHITE / 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: 40325 / Num. obs: 40325 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 17.3
Reflection shellResolution: 1.2→1.24 Å / Mean I/σ(I) obs: 14 / Rsym value: 0.09 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FB2

1fb2


Resolution: 1.2→17.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.853 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21705 824 2 %RANDOM
Rwork0.20934 ---
all0.2147 40325 --
obs0.20949 39501 100 %-
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: 14.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.1531 Å
Refinement stepCycle: LAST / Resolution: 1.2→17.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 15 270 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211050
X-RAY DIFFRACTIONr_bond_other_d0.0020.02887
X-RAY DIFFRACTIONr_angle_refined_deg1.5422.0011421
X-RAY DIFFRACTIONr_angle_other_deg0.83332093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9173132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24915201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021126
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02216
X-RAY DIFFRACTIONr_nbd_refined0.4090.3326
X-RAY DIFFRACTIONr_nbd_other0.2160.3964
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.5116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.5637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40121026
X-RAY DIFFRACTIONr_scbond_it1.663413
X-RAY DIFFRACTIONr_scangle_it2.4524.5395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 57
Rwork0.278 2912

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