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(-) Description

Title :  SIMULTANEOUS INHIBITION OF ANTI-COAGULATION AND INFLAMMATION: CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 COMPLEXED WITH INDOMETHACIN AT 1.4 A RESOLUTION REVEALS THE PRESENCE OF THE NEW COMMON LIGAND BINDING SITE
 
Authors :  N. Singh, R. Prem Kumar, S. Sharma, P. Kaur, T. P. Singh
Date :  29 Dec 08  (Deposition) - 20 Jan 09  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Pla2, Anti-Inflammatory, Anti-Coagulant, Indomethacin, Crystal Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Singh, R. Prem Kumar, S. Sharma, P. Kaur, T. P. Singh
Simultaneous Inhibition Of Anti-Coagulation And Inflammation: Crystal Structure Of Phospholipase A2 Complexed With Indomethacin At 1. 4 A Resolution Reveals The Presence Of The New Common Ligand Binding Site
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 VRV-PL-VIIIA
    Chains: A
    EC Number: 3.1.1.4
    Organism Scientific: DABOIA RUSSELLI PULCHELLA
    Organism Taxid: 97228
    Synonym: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, DPLA2, P1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1IMN1Ligand/IonINDOMETHACIN
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:1 , LEU A:3 , GLU A:4 , ARG A:72 , HOH A:139 , HOH A:307BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREARG A:43 , ARG A:72BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARESER A:90 , ASN A:93 , HOH A:199 , HOH A:262 , HOH A:303 , HOH A:329BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWARETYR A:113 , SER A:114 , LYS A:115 , LYS A:131BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWAREASP A:49 , TYR A:52 , ASN A:54 , PRO A:56 , CYS A:61 , PRO A:68 , LYS A:69 , HOH A:154 , HOH A:229 , HOH A:231BINDING SITE FOR RESIDUE IMN A 301

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:19 -Pro A:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FO7)

(-) Exons   (0, 0)

(no "Exon" information available for 3FO7)

(-) 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:121
 aligned with D0VX11_9SAUR | D0VX11 from UniProtKB/TrEMBL  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
         D0VX11_9SAUR     1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 121
               SCOP domains d3fo7a_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3fo7A00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo7 A   1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131|
                                        14|                                      56|||                 86|                               122|    131|
                                         16                                       59||                  88                                124     133
                                                                                   61|                                                               
                                                                                    67
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  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  (0, 0)

(no "Pfam Domain" information available for 3FO7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0VX11_9SAUR | D0VX11)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        D0VX11_9SAUR | D0VX11: 1q6v 1q7a 2arm 4eix 4fga 4gfy 4gld 4hmb 4qem 4qer 4qf7 4qf8 4qgd 4qmc

(-) Related Entries Specified in the PDB File

1fb2 NATIVE STRUCTURE