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- PDB-1pir: SOLUTION STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1pir
TitleSOLUTION STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE / PHOSPHOLIPASE A2 / PHOSPHATIDE-2-ACYL-HYDROLASE / PLA2
Function / homology
Function and homology information


regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity ...regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of immune response / phospholipid binding / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / positive regulation of MAPK cascade / 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
Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR
AuthorsVan Den Berg, B.D. / Tessari, M. / De Haas, G.H. / Verheij, H.M. / Boelens, R. / Kaptein, R.
CitationJournal: EMBO J. / Year: 1995
Title: Solution structure of porcine pancreatic phospholipase A2.
Authors: van den Berg, B. / Tessari, M. / de Haas, G.H. / Verheij, H.M. / Boelens, R. / Kaptein, R.
History
DepositionDec 22, 1994Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0502
Polymers14,0101
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: GLN 4 - PHE 5 OMEGA = 149.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY 33 - SER 34 OMEGA = 213.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: SER 34 - GLY 35 OMEGA = 143.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY 35 - THR 36 OMEGA = 138.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: VAL 38 - ASP 39 OMEGA = 141.85 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: LEU 41 - ASP 42 OMEGA = 136.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ASN 57 - LEU 58 OMEGA = 223.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: PHE 63 - LEU 64 OMEGA = 114.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: GLU 71 - SER 72 OMEGA = 213.52 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: CYS 77 - SER 78 OMEGA = 31.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION RESIDUE CYS 77 IS A CIS-PEPTIDE IN THE AVERAGED STRUCTURE.
11: ASN 79 - THR 80 OMEGA = 102.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ASN 85 - SER 86 OMEGA = 219.82 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: SER 86 - LYS 87 OMEGA = 140.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: ASN 101 - ALA 102 OMEGA = 145.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: ALA 109 - PRO 110 OMEGA = 140.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
16: LYS 113 - GLU 114 OMEGA = 232.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: LYS 116 - ASN 117 OMEGA = 144.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
18: ASN 117 - LEU 118 OMEGA = 213.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: ASP 119 - THR 120 OMEGA = 226.20 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: THR 120 - LYS 121 OMEGA = 123.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 14009.714 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

NMR ensembleConformers submitted total number: 1

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