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- PDB-1db5: HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6 -

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Basic information

Entry
Database: PDB / ID: 1db5
TitleHUMAN S-PLA2 IN COMPLEX WITH INDOLE 6
ComponentsPROTEIN (PHOSPHOLIPASE A2)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / S-PLA2 / STRUCTURE-BASED DRUG DESIGN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / intestinal stem cell homeostasis / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / intestinal stem cell homeostasis / Synthesis of PA / phospholipase A2 activity / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / low-density lipoprotein particle remodeling / phospholipase A2 / positive regulation of macrophage derived foam cell differentiation / calcium-dependent phospholipase A2 activity / Antimicrobial peptides / arachidonate secretion / lipid catabolic process / phospholipid metabolic 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 / 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
Chem-6IN / Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsChirgadze, N.Y. / Schevitz, R.W. / Wery, J.-P.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2.
Authors: Schevitz, R.W. / Bach, N.J. / Carlson, D.G. / Chirgadze, N.Y. / Clawson, D.K. / Dillard, R.D. / Draheim, S.E. / Hartley, L.W. / Jones, N.D. / Mihelich, E.D. / Olkowski, J.L. / Snyder, D.W. / ...Authors: Schevitz, R.W. / Bach, N.J. / Carlson, D.G. / Chirgadze, N.Y. / Clawson, D.K. / Dillard, R.D. / Draheim, S.E. / Hartley, L.W. / Jones, N.D. / Mihelich, E.D. / Olkowski, J.L. / Snyder, D.W. / Sommers, C. / Wery, J.-P.
History
DepositionNov 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Oct 30, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOLIPASE A2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4064
Polymers13,9451
Non-polymers4613
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.360, 76.360, 91.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PROTEIN (PHOSPHOLIPASE A2)


Mass: 13945.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P14555, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-6IN / 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID


Mass: 380.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7
Details: 10 mg/ml of protein; 50 mM buffer (MES or MOPS), 1% pyridine., pH 7.0, VAPOR DIFFUSION, temperature 297K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMMES1dropor MOPS
380-92 %satsodium chloride1drop
41 %pyridine1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 3, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 4159 / % possible obs: 97.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.3 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 70 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98refinement
X-PLORphasing
RefinementResolution: 2.8→30 Å / Data cutoff high absF: 0.001 / Data cutoff low absF: 1000000 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 209 5.4 %RANDOM
Rwork0.196 ---
obs0.196 3933 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 30 38 1034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.736
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 24 5.4 %
Rwork0.299 436 -
obs--94.7 %
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.4 % / Rfactor obs: 0.172 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.736
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.299

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