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(-) Description

Title :  GLN48 PLA2 SEPARATED FROM VIPOXIN FROM THE VENOM OF VIPERA AMMODYTES MERIDIONALIS.
 
Authors :  D. N. Georgieva, M. Perbandt, W. Rypniewski, K. Hristov, N. Genov, C. Betzel
Date :  11 Aug 03  (Deposition) - 04 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. N. Georgieva, M. Perbandt, W. Rypniewski, K. Hristov, N. Genov, C. Betzel
The X-Ray Structure Of A Snake Venom Gln48 Phospholipase A2 At 1. 9A Resolution Reveals Anion-Binding Sites.
Biochem. Biophys. Res. Commun. V. 316 33 2004
PubMed-ID: 15003507  |  Reference-DOI: 10.1016/J.BBRC.2004.01.174
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 INHIBITOR
    Chains: A, B
    Organism Scientific: VIPERA AMMODYTES MERIDIONALIS
    Organism Taxid: 73841
    Secretion: VENOM
    Strain: MERIDIONALIS
    Synonym: VIPOXIN TOXIC COMPONENT, VIPOXIN A CHAIN, INH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , ARG A:36 , GLN A:38 , TYR A:120 , HIS A:125 , CYS A:126 , THR A:127 , GLU A:128BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREALA A:40 , ARG A:43 , HOH A:481 , HOH A:554 , ASN B:111BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREGLY B:35 , ARG B:36 , GLN B:38 , TYR B:120 , HIS B:125 , CYS B:126 , THR B:127 , GLU B:128BINDING SITE FOR RESIDUE SO4 B 403
4AC4SOFTWAREARG A:54 , ASP A:89 , LEU A:90 , CYS A:91 , HOH A:494 , HOH A:496BINDING SITE FOR RESIDUE SO4 A 404

(-) SS Bonds  (14, 14)

Asymmetric 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
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5T)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95
 		  2A:95-105
B:95-105
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95
 		  2A:95-105
B:95-105
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95
 		  4A:95-105
B:95-105
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95
 		  4A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1Q5T)

(-) Sequences/Alignments

Asymmetric 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 PA2A_VIPAE | P04084 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:123
                                                                                   56                                                                  
                                                                                 55 |                                                                  
                                    10        20        30        40        50    | | 59        69        79        89        99       109       119   
           PA2A_VIPAE     1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRVN-DCNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 122
               SCOP domains d1q5ta_ A: Snake phospholipase A2                                                                                           SCOP domains
               CATH domains 1q5tA00 A:1-133 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhh.............hhhhhhhhhhhhhhh....-.........eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5t A   1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRNLV-CNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 133
                                    10   ||   21        31        41        51    || |68        78       |89        99       109       119  ||   130   
                                        14|                                      56| ||                 86|                               122|         
                                         16                                       59 ||                  88                                124         
                                                                                    61|                                                                
                                                                                     67                                                                


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2A_VIPAE | P04084 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:123
                                                                                   56                                                                  
                                                                                 55 |                                                                  
                                    10        20        30        40        50    | | 59        69        79        89        99       109       119   
           PA2A_VIPAE     1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRVN-DCNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 122
               SCOP domains d1q5tb_ B: Snake phospholipase A2                                                                                           SCOP domains
               CATH domains 1q5tB00 B:1-133 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhh.............hhhhhhhhhhhhhhhh...-.........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q5t B   1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRNLV-CNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 133
                                    10   ||   21        31        41        51    || |68        78       |89        99       109       119  ||   130   
                                        14|                                      56| ||                 86|                               122|         
                                         16                                       59 ||                  88                                124         
                                                                                    61|                                                                
                                                                                     67
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q5T)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PA2A_VIPAE | P04084)
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.
    GO:0035792    other organism postsynaptic membrane    A postsynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A postsynaptic membrane is a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters transmit the signal across the synaptic cleft to the postsynaptic membrane.

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  1q5t
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 Related Entries

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UniProtKB/Swiss-Prot
        PA2A_VIPAE | P04084: 1aok 1jlt 1vpi

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