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- PDB-5p2p: X-RAY STRUCTURE OF PHOSPHOLIPASE A2 COMPLEXED WITH A SUBSTRATE-DE... -

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Basic information

Entry
Database: PDB / ID: 5p2p
TitleX-RAY STRUCTURE OF PHOSPHOLIPASE A2 COMPLEXED WITH A SUBSTRATE-DERIVED INHIBITOR
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE(CARBOXYLIC ESTER)
Function / homology
Function and homology information


positive regulation of podocyte apoptotic process / regulation of D-glucose import / phospholipase A2 activity / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-independent phospholipase A2 activity ...positive regulation of podocyte apoptotic process / regulation of D-glucose import / phospholipase A2 activity / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-independent phospholipase A2 activity / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity / positive regulation of interleukin-8 production / phospholipid binding / positive regulation of immune response / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / cell surface / positive regulation of transcription by RNA polymerase II / 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
Chem-DHG / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsDijkstra, B.W. / Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J.
Citation
Journal: Nature / Year: 1990
Title: X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor.
Authors: Thunnissen, M.M. / Ab, E. / Kalk, K.H. / Drenth, J. / Dijkstra, B.W. / Kuipers, O.P. / Dijkman, R. / de Haas, G.H. / Verheij, H.M.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Structure of an Engineered Porcine Phospholipase A2 with Enhanced Activity at 2.1 Angstroms Resolution. Comparison with the Wild-Type Porcine and Crotalus Atrox PhospholipaseA2
Authors: Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J. / Dijkstra, B.W.
#2: Journal: Science / Year: 1989
Title: Enhanced Activity and Altered Specificity of Phospholipase A2 by Deletion of a Surface Loop
Authors: Kuipers, O.P. / Thunnissen, M.M.G.M. / Degeus, P. / Dijkstra, B.W. / Drenth, J. / Verheij, H.M. / Dehaas, G.H.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2
Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution
Authors: Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J.
#5: Journal: Nature / Year: 1981
Title: Active Site and Catalytic Mechanism of Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H.
History
DepositionSep 1, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8297
Polymers26,8622
Non-polymers9675
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-44 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.570, 62.440, 85.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CALCIUM 1 LIES ON A NONCRYSTALLOGRAPHIC LOCAL TWO-FOLD AXIS.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999045, 0.043367, 0.005395), (-0.018846, -0.31616, -0.948519), (-0.039429, -0.947714, 0.316676)
Vector: -18.551, -20.243, -14.914)
DetailsTHE ENZYME CRYSTALLIZES AS A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION GIVEN ON *MTRIX* RECORDS BELOW YIELDS OPTIMAL CARBON-ALPHA COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE RMS DIFFERENCE FOR ALL 119 CARBON-ALPHA PAIRS IS 0.228 ANGSTROMS.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13431.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DHG / PHOSPHONIC ACID 2-DODECANOYLAMINO-HEXYL ESTER PROPYL ESTER


Mass: 423.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 %MPD1reservoir
2100 mMTris-HCl1reservior
35 mM1reservoirCaCl2
41 mg/mlinhibitor1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 89.1 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.189 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 59 126 2047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 7 Å / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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