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(-) Description

Title :  CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2
 
Authors :  Y. Matoba, Y. Katsube, M. Sugiyama
Date :  28 Dec 01  (Deposition) - 04 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipase A2, Prokaryote, Calcium Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, Y. Katsube, M. Sugiyama
The Crystal Structure Of Prokaryotic Phospholipase A2.
J. Biol. Chem. V. 277 20059 2002
PubMed-ID: 11897785  |  Reference-DOI: 10.1074/JBC.M200263200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A
    EC Number: 3.1.1.4
    Engineered: YES
    Expression System: STREPTOMYCES LIVIDANS TK24
    Expression System Plasmid: PIJ680
    Expression System Strain: TK24
    Expression System Taxid: 457428
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES VIOLACEORUBER
    Organism Taxid: 1935

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , LEU A:44 , ASP A:65 , HOH A:201 , HOH A:202 , HOH A:203BINDING SITE FOR RESIDUE CA A 200

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:61
2A:96 -A:107

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KP4)

(-) Exons   (0, 0)

(no "Exon" information available for 1KP4)

(-) 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 A from PDB  Type:PROTEIN  Length:122
 aligned with Q6UV28_STRVN | Q6UV28 from UniProtKB/TrEMBL  Length:150

    Alignment length:122
                                                                                                                                                  150 
                                    39        49        59        69        79        89        99       109       119       129       139       149| 
         Q6UV28_STRVN    30 APADKPQVLASFTQTSASSQNAWLAANRNQSAWAAYEFDWSTDLCSQAPDNPFGFPFNTACARHDFGYRNYKAAGSFDANKSRIDSAFYEDMKRVCTGYTGEKNTACNSTAWTYYQAVKIL-   -
               SCOP domains d1kp4a_ A: Prokaryotic phospholipase A2                                                                                    SCOP domains
               CATH domains 1kp4A00 A:1-122 Phospholipase A2                                                                                           CATH domains
               Pfam domains ------------Phospholip_A2_3-1kp4A01 A:13-120                                                                            -- Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kp4 A   1 APADKPQVLASFTQTSASSQNAWLAANRNQSAWAAYEFDWSTDLCTQAPDNPFGFPFNTACARHDFGYRNYKAAGSFDANKSRIDSAFYEDMKRVCTGYTGEKNTACNSTAWTYYQAVKIFG 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain A from PDB  Type:PROTEIN  Length:122
 aligned with Q9Z4W2_STRCO | Q9Z4W2 from UniProtKB/TrEMBL  Length:151

    Alignment length:122
                                    39        49        59        69        79        89        99       109       119       129       139       149  
         Q9Z4W2_STRCO    30 APADKPQVLASFTQTSASSQNAWLAANRNQSAWAAYEFDWSTDLCTQAPDNPFGFPFNTACARHDFGYRNYKAAGSFDANKSRIDSAFYEDMKRVCTGYTGEKNTACNSTAWTYYQAVKIFG 151
               SCOP domains d1kp4a_ A: Prokaryotic phospholipase A2                                                                                    SCOP domains
               CATH domains 1kp4A00 A:1-122 Phospholipase A2                                                                                           CATH domains
               Pfam domains ------------Phospholip_A2_3-1kp4A01 A:13-120                                                                            -- Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kp4 A   1 APADKPQVLASFTQTSASSQNAWLAANRNQSAWAAYEFDWSTDLCTQAPDNPFGFPFNTACARHDFGYRNYKAAGSFDANKSRIDSAFYEDMKRVCTGYTGEKNTACNSTAWTYYQAVKIFG 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Phospholip_A2_3] (2)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9Z4W2_STRCO | Q9Z4W2)

Chain A   (Q6UV28_STRVN | Q6UV28)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  1kp4
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  3.1.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Z4W2_STRCO | Q9Z4W2: 1faz 1it4 1lwb
UniProtKB/TrEMBL
        Q6UV28_STRVN | Q6UV28: 1faz 1it4 1it5 1lwb

(-) Related Entries Specified in the PDB File

1faz 1FAZ CONTAINS CALCIUM-FREE FORM OF PROKARYOTIC PHOSPHOLIPASE A2
1it4 1IT4 CONTAINS SOLUTION STRUCTURE OF CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2
1it5 1IT5 CONTAINS SOLUTION STRUCTURE OF CALCIUM-FREE FORM OF PROKARYOTIC PHOSPHOLIPASE A2