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Asym./Biol. Unit (Jmol Viewer)

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Title :   PIRATOXIN-II (PRTX-II) - A K49 PLA2 FROM BOTHROPS PIRAJAI

Authors :   W. -H. Lee, I. Polikarpov

Date :   01 Sep 99 (Deposition) - 07 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym./Biol. Unit : A,B

Keywords :   Neurotoxin, K49 Phospholipase A2 (Pla2) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. H. Lee, M. T. Da Silva Giotto, S. Marangoni, M. H. Toyama, I. Polikarpov, R. C. Garratt
Structural Basis For Low Catalytic Activity In Lys49 Phospholipases A2-A Hypothesis: The Crystal Structure Of Piratoxin Ii Complexed To Fatty Acid
Biochemistry V. 40 28 2001
PubMed-ID: 11141053 | Reference-DOI: 10.1021/BI0010470

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Organism Scientific	:	BOTHROPS PIRAJAI
	Organism Taxid	:	113192
	Other Details	:	FATTY ACID TRAPPED AT THE HYDROPHOBIC CHANNEL
	Secretion	:	TOTAL VENOM
	Synonym	:	MYOTOXIN II, BOTHROPSTOXIN I, BTXTX1, BTHTX1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	TDA	2	Ligand/Ion	N-TRIDECANOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:2 , GLY A:6 , ILE A:9 , PRO A:17 , TYR A:21 , CYS A:28 , GLY A:29 , HIS A:47 , HOH A:2002 , HOH A:2149 , HOH A:2150	BINDING SITE FOR RESIDUE TDA A 122
2	AC2	SOFTWARE	LEU B:2 , GLY B:6 , ILE B:9 , PRO B:17 , TYR B:21 , CYS B:28 , GLY B:29 , HIS B:47 , HOH B:2001 , HOH B:2152	BINDING SITE FOR RESIDUE TDA B 122

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:115
2	A:28	-	A:44
3	A:43	-	A:95
4	A:49	-	A:121
5	A:50	-	A:88
6	A:57	-	A:81
7	A:75	-	A:86
8	B:26	-	B:115
9	B:28	-	B:44
10	B:43	-	B:95
11	B:49	-	B:121
12	B:50	-	B:88
13	B:57	-	B:81
14	B:75	-	B:86

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H2_BOTPI	43-50	2	A:43-50 B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H2_BOTPI	85-95	2	A:85-95 B:85-95

(no "Exon" information available for 1QLL)

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 PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d1qlla_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1qllA00 A:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qll A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADKC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H2_BOTPI | P82287 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H2_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 121
               SCOP domains d1qllb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1qllB00 B:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qll B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADKC 121
                                    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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Phospholipase A2, PLA2 (282)

Superfamily: Phospholipase A2, PLA2 (282)

Family: Vertebrate phospholipase A2 (271)

Protein domain: Snake phospholipase A2 (124)

Bothrops pirajai, Piratoxin-II (PRTX-II) [TaxId: 113192] (3)

1a	d1qlla_	A:
1b	d1qllb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Phospholipase A2 (241)

Homologous Superfamily: Phospholipase A2 (241)

Bothrops pirajai. Organism_taxid: 113192. (1)

1a	1qllA00	A:1-121
1b	1qllB00	B:1-121

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2H2_BOTPI | P82287)

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.

Asymmetric/Biological Unit
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	PA2H2_BOTPI \| P82287	:	2q2j 3cyl

1clp	MYOTOXIN II (PHOSPHOLIPASE A2) (E.C.3.1.1.4) MUTANT WITH ASP 49 REPLACED BY LYS (D49K) FROM TERCIOPELO (BOTHROPS ASPER)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (14, 14)

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