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- PDB-5g3n: Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. -

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Basic information

Entry
Database: PDB / ID: 5g3n
TitleDiscovery of a novel secreted phospholipase A2 (sPLA2) inhibitor.
ComponentsPHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
KeywordsHYDROLASE / SPLA2 / SECRETED PHOSPHOLIPASE A2 / CARDIOVASCULAR DISEASE / INHIBITOR / FRAGMENT
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylcholine metabolic process / positive regulation of macrophage derived foam cell differentiation / phospholipase A2 activity / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / phospholipase A2 / Antimicrobial peptides / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / secretory granule / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
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
FORMIC ACID / Chem-X28 / Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSandmark, J. / Bodin, C. / Hallberg, K.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Discovery of Azd2716: A Novel Secreted Phospholipase A2 (Spla2) Inhibitor for the Treatment of Coronary Artery Disease
Authors: Giordanetto, F. / Pettersen, D. / Starke, I. / Nordberg, P. / Dahlstrom, M. / Knerr, L. / Selmi, N. / Rosengren, B. / Larsson, L.O. / Sandmark, J. / Castaldo, M. / Dekker, N. / Karlsson, U. / Hurt-Camejo, E.
History
DepositionApr 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
B: PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,41410
Polymers28,4432
Non-polymers9718
Water4,089227
1
A: PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7075
Polymers14,2211
Non-polymers4864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7075
Polymers14,2211
Non-polymers4864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 66.530, 73.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3229, -0.9462, -0.01958), (0.9463, -0.3231, 0.008015), (-0.01391, -0.01595, 0.9998)
Vector: 40.31, 22.81, 4.811)

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Components

#1: Protein PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED / 3SECRETED PHOSPHOLIPASE A2 TYPE IIA / GIIC SPLA2 / GROUP IIA PHOSPHOLIPASE A2 / NON-PANCREATIC ...3SECRETED PHOSPHOLIPASE A2 TYPE IIA / GIIC SPLA2 / GROUP IIA PHOSPHOLIPASE A2 / NON-PANCREATIC SECRETORY PHOSPHOLIPASE A2 / NPS-PLA2 / PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE 2A


Mass: 14221.306 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14555, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-X28 / 3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID


Mass: 359.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H21NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN1A, T76A MUTATION

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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: 2.25 Å3/Da / Density % sol: 45.27 % / Description: NONE
Crystal growDetails: 3.0-3.5M SODIUM FORMATE AND 100MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.6 Å / Num. obs: 23401 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.64 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 1.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.56 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9278 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.129
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2234. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2234. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1201 5.14 %RANDOM
Rwork0.1947 ---
obs0.1966 23380 95.92 %-
Displacement parametersBiso mean: 25.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.5781 Å20 Å20 Å2
2---0.6992 Å20 Å2
3----0.879 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 64 227 2238
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082757HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d727SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2061HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion18.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion250SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2555SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3285 148 5.31 %
Rwork0.3034 2640 -
all0.3048 2788 -
obs--95.92 %

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