Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER
 
Authors :  S. Brunie, P. B. Sigler
Date :  10 Mar 86  (Deposition) - 07 May 86  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  L,R
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Brunie, J. Bolin, D. Gewirth, P. B. Sigler
The Refined Crystal Structure Of Dimeric Phospholipase A2 At 2. 5 A. Access To A Shielded Catalytic Center.
J. Biol. Chem. V. 260 9742 1985
PubMed-ID: 4019493
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALCIUM-FREE PHOSPHOLIPASE A2
    Chains: R, L
    EC Number: 3.1.1.4
    Engineered: YES
    Organism Common: WESTERN DIAMONDBACK RATTLESNAKE
    Organism Scientific: CROTALUS ATROX
    Organism Taxid: 8730

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : LR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PP2)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1ANLAUTHORSER L:1 , GLN L:4 , VAL L:71 , TYR L:73RESIDUES FORMING THE ACTIVATION NETWORK
2ANRAUTHORSER R:1 , GLN R:4 , VAL R:71 , TYR R:73RESIDUES FORMING THE ACTIVATION NETWORK
3CALAUTHORTYR L:28 , GLY L:30 , GLY L:32 , ASP L:49RESIDUES FORMING THE CA2+ BINDING SITE DEDUCED FROM BOVINE STRUCTURE
4CARAUTHORTYR R:28 , GLY R:30 , GLY R:32 , ASP R:49RESIDUES FORMING THE CA2+ BINDING SITE DEDUCED FROM BOVINE STRUCTURE
5CNLAUTHORHIS L:48 , TYR L:52 , TYR L:73 , ASP L:99RESIDUES FORMING THE CATALYTIC NETWORK
6CNRAUTHORHIS R:48 , TYR R:52 , TYR R:73 , ASP R:99RESIDUES FORMING THE CATALYTIC NETWORK

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1L:27 -L:126
2L:29 -L:45
3L:44 -L:105
4L:50 -L:133
5L:51 -L:98
6L:61 -L:91
7L:84 -L:96
8R:27 -R:126
9R:29 -R:45
10R:44 -R:105
11R:50 -R:133
12R:51 -R:98
13R:61 -R:91
14R:84 -R:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PP2)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A_CROAT59-66
 		  2L:44-51
R:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_CROAT101-111
 		  2L:95-105
R:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1PP2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain L from PDB  Type:PROTEIN  Length:122
 aligned with PA2A_CROAT | P00624 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
           PA2A_CROAT    17 SLVQFETLIMKIAGRSGLLWYSAYGCYCGWGGHGLPQDATDRCCFVHDCCYGKATDCNPKTVSYTYSEENGEIICGGDDPCGTQICECDKAAAICFRDNIPSYDNKYWLFPPKNCREEPEPC 138
               SCOP domains d1pp2l_ L: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1pp2L00 L:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhh..................hhhhhhhhhhhhhh...........eeee....eeee...hhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pp2 L   1 SLVQFETLIMKIAGRSGLLWYSAYGCYCGWGGHGLPQDATDRCCFVHDCCYGKATDCNPKTVSYTYSEENGEIICGGDDPCGTQICECDKAAAICFRDNIPSYDNKYWLFPPKDCREEPEPC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67                                                                


Chain R from PDB  Type:PROTEIN  Length:122
 aligned with PA2A_CROAT | P00624 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
           PA2A_CROAT    17 SLVQFETLIMKIAGRSGLLWYSAYGCYCGWGGHGLPQDATDRCCFVHDCCYGKATDCNPKTVSYTYSEENGEIICGGDDPCGTQICECDKAAAICFRDNIPSYDNKYWLFPPKNCREEPEPC 138
               SCOP domains d1pp2r_ R: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1pp2R00 R:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....hhhh..................hhhhhhhhhhhhhh...........eeee....eeee...hhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pp2 R   1 SLVQFETLIMKIAGRSGLLWYSAYGCYCGWGGHGLPQDATDRCCFVHDCCYGKATDCNPKTVSYTYSEENGEIICGGDDPCGTQICECDKAAAICFRDNIPSYDNKYWLFPPKDCREEPEPC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PP2)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L,R   (PA2A_CROAT | P00624)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pp2)
 
  Sites
    ANL  [ RasMol ]  +environment [ RasMol ]
    ANR  [ RasMol ]  +environment [ RasMol ]
    CAL  [ RasMol ]  +environment [ RasMol ]
    CAR  [ RasMol ]  +environment [ RasMol ]
    CNL  [ RasMol ]  +environment [ RasMol ]
    CNR  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pp2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pp2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PA2A_CROAT | P00624
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.1.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PA2A_CROAT | P00624
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1PP2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PP2)