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- PDB-1oxl: INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PRO... -

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Basic information

Entry
Database: PDB / ID: 1oxl
TitleINHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION
ComponentsPhospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE / phospholipase A2 / indole derivative / inhibition
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBONATE ION / Chem-IDA / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii russellii (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChandra, V. / Balasubramanya, R. / Kaur, P. / Singh, T.P.
Citation
Journal: Biochim.Biophys.Acta / Year: 2005
Title: Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic ...Title: Crystal structure of the complex of the secretory phospholipase A2 from Daboia russelli pulchella with an endogenic indole derivative, 2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl-acetic acid at 1.8 A resolution.
Authors: Balasubramanya, R. / Chandra, V. / Kaur, P. / Singh, T.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Regulation of catalytic function by molecular association: Crystal structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 resolution
Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C.H. / Singh, T.P.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from daboia russelli pulchella at 2.4 resolution
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / Singh, T.P.
History
DepositionApr 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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 / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 16, 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
Revision 1.6Oct 9, 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 VRV-PL-VIIIa
B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7506
Polymers27,2602
Non-polymers4904
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-21 kcal/mol
Surface area12820 Å2
MethodPISA
2
B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules

B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules

A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules

A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,50012
Polymers54,5194
Non-polymers9818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area5040 Å2
ΔGint-69 kcal/mol
Surface area25640 Å2
MethodPISA
3
B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules

A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7506
Polymers27,2602
Non-polymers4904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area1010 Å2
ΔGint-23 kcal/mol
Surface area14330 Å2
MethodPISA
4
B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules

A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7506
Polymers27,2602
Non-polymers4904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
Buried area1780 Å2
ΔGint-22 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.020, 88.442, 78.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-542-

HOH

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Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa / Phosphatidylcholine 2- acylhydrolase


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Secretion: venom / Species: Daboia russellii / Strain: russellii / References: UniProt: P59071, phospholipase A2
#2: Chemical ChemComp-IDA / (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)ACETIC ACID


Mass: 274.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O3
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2001 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 21615 / Num. obs: 21615 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23.59 Å2 / Rsym value: 0.031 / Net I/σ(I): 39.9
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.083 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FB2

1fb2


Resolution: 1.8→19.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.697 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23816 1166 5.1 %RANDOM
Rwork0.1881 ---
all0.19059 21615 --
obs0.19059 21615 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: 24.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.41 Å20 Å2
3---1.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 33 284 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211964
X-RAY DIFFRACTIONr_bond_other_d0.0010.021665
X-RAY DIFFRACTIONr_angle_refined_deg1.8612.0042630
X-RAY DIFFRACTIONr_angle_other_deg1.04733931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6943232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.18515364
X-RAY DIFFRACTIONr_chiral_restr0.0850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
X-RAY DIFFRACTIONr_nbd_refined0.3520.3509
X-RAY DIFFRACTIONr_nbd_other0.2170.31581
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.526
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2020.52
X-RAY DIFFRACTIONr_mcbond_it0.7471.51195
X-RAY DIFFRACTIONr_mcangle_it1.40421885
X-RAY DIFFRACTIONr_scbond_it1.9483769
X-RAY DIFFRACTIONr_scangle_it3.1414.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 114
Rwork0.199 1539

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