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- PDB-1td7: Interactions of a specific non-steroidal anti-inflammatory drug (... -

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Basic information

Entry
Database: PDB / ID: 1td7
TitleInteractions of a specific non-steroidal anti-inflammatory drug (NSAID) with group I phospholipase A2 (PLA2): Crystal structure of the complex formed between PLA2 and niflumic acid at 2.5 A resolution
ComponentsPhospholipase A2 isoform 3
KeywordsHYDROLASE / Phospholipase A2 / Enzyme / Inhibitor
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
Chem-NFL / Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJabeen, T. / Singh, N. / Singh, R.K. / Sharma, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2 with niflumic acid at 2.5 Angstroms resolution.
Authors: Jabeen, T. / Singh, N. / Singh, R.K. / Sharma, S. / Somvanshi, R.K. / Dey, S. / Singh, T.P.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Phospholipase A2 isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5063
Polymers13,1841
Non-polymers3222
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.356, 42.356, 64.958
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 / Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase


Mass: 13183.592 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NFL / 2-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}NICOTINIC ACID / 2-[(3-TRIFLUOROMETHYL)PHENYL]AMINO-3-PYRIDINE-CARBOXYLIC ACID / Niflumic acid


Mass: 282.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F3N2O2 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10mM Sodium Phosphate, 2mM CaCl2, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004 / Details: monochromator
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 4004 / Num. obs: 4004 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 20.6
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 7.5 / Num. unique all: 4004 / Rsym value: 0.238 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF4

1mf4


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.371 / SU ML: 0.276 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24203 179 4.5 %RANDOM
Rwork0.19262 ---
all0.211 4004 --
obs0.19481 4004 99.73 %-
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: 27.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 21 101 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021960
X-RAY DIFFRACTIONr_bond_other_d0.0010.02751
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9641305
X-RAY DIFFRACTIONr_angle_other_deg0.93231761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3823117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92115145
X-RAY DIFFRACTIONr_chiral_restr0.10.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021105
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02204
X-RAY DIFFRACTIONr_nbd_refined0.3210.3297
X-RAY DIFFRACTIONr_nbd_other0.2310.3804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5100
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.54
X-RAY DIFFRACTIONr_mcbond_it0.7691.5589
X-RAY DIFFRACTIONr_mcangle_it1.5072935
X-RAY DIFFRACTIONr_scbond_it2.063371
X-RAY DIFFRACTIONr_scangle_it3.4114.5370
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.232 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 13 -
Rwork0.211 257 -
obs-386 99.5 %

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