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- PDB-6g5j: Secreted phospholipase A2 type X in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 6g5j
TitleSecreted phospholipase A2 type X in complex with ligand
ComponentsGroup 10 secretory phospholipase A2
KeywordsHYDROLASE / SECRETORY PHOSPHOLIPASE A2 TYPE X sPLA2X sPLA2-X phospholipase enzyme inhibitor complex
Function / homology
Function and homology information


phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / Acyl chain remodelling of PC / phospholipase activity ...phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / Acyl chain remodelling of PC / phospholipase activity / Acyl chain remodelling of PI / intestinal stem cell homeostasis / Acyl chain remodelling of PS / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / negative regulation of cholesterol efflux / arachidonate metabolic process / phosphatidylglycerol metabolic process / phosphatidylcholine catabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / positive regulation of prostaglandin secretion / positive regulation of arachidonate secretion / macrophage activation / low-density lipoprotein particle remodeling / fertilization / phospholipase A2 / calcium-dependent phospholipase A2 activity / prostaglandin biosynthetic process / arachidonate secretion / regulation of macrophage activation / hair follicle morphogenesis / erythrocyte maturation / negative regulation of cytokine production involved in inflammatory response / phospholipid metabolic process / positive regulation of protein metabolic process / acrosomal vesicle / cholesterol homeostasis / cellular response to leukemia inhibitory factor / axon guidance / negative regulation of DNA-binding transcription factor activity / phospholipid binding / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / extracellular space / 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
Chem-EM8 / DI(HYDROXYETHYL)ETHER / Group 10 secretory phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsSandmark, J. / Oster, L.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Design of Selective sPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1H-indol-1-yl]pyridine-2-yl}propanoic Acid.
Authors: Giordanetto, F. / Knerr, L. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Mansson, A. / Dahlstrom, M. / Broddefalk, J. / Saarinen, G. / Klingegard, F. / Hurt- ...Authors: Giordanetto, F. / Knerr, L. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Mansson, A. / Dahlstrom, M. / Broddefalk, J. / Saarinen, G. / Klingegard, F. / Hurt-Camejo, E. / Rosengren, B. / Wikstrom, J. / Wagberg, M. / Brengdahl, J. / Rohman, M. / Sandmark, J. / Akerud, T. / Roth, R.G. / Jansen, F. / Ahlqvist, M.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group 10 secretory phospholipase A2
B: Group 10 secretory phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8269
Polymers36,3432
Non-polymers1,4837
Water2,450136
1
A: Group 10 secretory phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2086
Polymers18,1711
Non-polymers1,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group 10 secretory phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6183
Polymers18,1711
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.962, 85.501, 103.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Group 10 secretory phospholipase A2 / Group X secretory phospholipase A2 / sPLA2-X / Phosphatidylcholine 2-acylhydrolase 10


Mass: 18171.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15496, phospholipase A2

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EM8 / (3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid


Mass: 406.355 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H17F3N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 37-45% PEG400 0.1M bis-Tris pH 5.6-5.9 / PH range: 5.6-5.9 / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→44.15 Å / Num. all: 71101 / Num. obs: 21588 / % possible obs: 91 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementResolution: 1.85→42.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.975 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22779 1060 5.1 %RANDOM
Rwork0.19392 ---
obs0.19568 19791 87.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.567 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.85→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 100 136 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192111
X-RAY DIFFRACTIONr_bond_other_d0.0020.021771
X-RAY DIFFRACTIONr_angle_refined_deg1.2872.0272888
X-RAY DIFFRACTIONr_angle_other_deg0.94634123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2715253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70524.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46815316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.874158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0252.183991
X-RAY DIFFRACTIONr_mcbond_other1.0192.18990
X-RAY DIFFRACTIONr_mcangle_it1.6333.2651239
X-RAY DIFFRACTIONr_mcangle_other1.6333.2691240
X-RAY DIFFRACTIONr_scbond_it1.4522.3951120
X-RAY DIFFRACTIONr_scbond_other1.4512.3961121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4133.5091646
X-RAY DIFFRACTIONr_long_range_B_refined3.8218.1812534
X-RAY DIFFRACTIONr_long_range_B_other3.8218.1812534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 52 -
Rwork0.305 1302 -
obs--78.31 %

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