3G8H - JenaLib

Title :   CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 AMMODYTOXIN C FROM VIPERA AMMODYTES AMMODYTES

Authors :   F. A. Saul, G. Faure

Date :   12 Feb 09 (Deposition) - 15 Dec 09 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Phospholipase A2, Ammodytoxin, Presynaptic Neurotoxin, Anticoagulant, Snake Venom, Hydrolase, Lipid Degradation, Metal-Binding, Secreted, Neurotoxin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. A. Saul, P. Prijatelj-Znidarsic, B. Vulliez-Le Normand, B. Villette, B. Raynal, J. Pungercar, I. Krizaj, G. Faure
Comparative Structural Studies Of Two Natural Isoforms Of Ammodytoxin, Phospholipases A2 From Vipera Ammodytes Ammodytes Which Differ In Neurotoxicity And Anticoagulant Activity
J. Struct. Biol. V. 169 360 2010
PubMed-ID: 19857576 | Reference-DOI: 10.1016/J.JSB.2009.10.010

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (7, 7)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BC_VIPAA	59-66	1	A:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BC_VIPAA	101-111	1	A:85-95

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BC_VIPAA	59-66	2	A:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BC_VIPAA	101-111	2	A:85-95

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with PA2BC_VIPAA | P11407 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BC_VIPAA    17 SLLEFGMMILGETGKNPLTSYSFYGCYCGVGGKGTPKDATDRCCFVHDCCYGNLPDCSPKTDRYKYHRENGAIVCGKGTSCENRICECDRAAAICFRKNLKTYNYIYRNYPDILCKEESEKC 138
               SCOP domains d3g8ha_ A: automated matches                                                                                               SCOP domains
               CATH domains 3g8hA00 A:1-122 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 ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g8h A   1 SLLEFGMMILGETGKNPLTSYSFYGCYCGVGGKGTPKDATDRCCFVHDCCYGNLPDCSPKTDRYKYHRENGAIVCGKGTSCENRICECDRAAAICFRKNLKTYNYIYRNYPDILCKEESEKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
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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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (PA2BC_VIPAA | P11407)

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.
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044164	host cell cytosol	The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0072556	other organism presynaptic membrane	A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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