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Title :   CRYSTAL STRUCTURE OF PRTX-I, A PLA2 HOMOLOG FROM BOTHROPS PIRAJAI

Authors :   J. I. Dos Santos, M. R. Fontes

Date :   28 May 07 (Deposition) - 10 Jun 08 (Release) - 22 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Myotoxin, Pla2 Like, Lys49-Pla2, Phospholipase A2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Dos Santos, A. M. Soares, M. R. Fontes
Comparative Structural Studies On Lys49-Phospholipases A(2) From Bothrops Genus Reveal Their Myotoxic Site.
J. Struct. Biol. V. 167 106 2009
PubMed-ID: 19401234 | Reference-DOI: 10.1016/J.JSB.2009.04.003
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 1
	Chains	:	A, B
	Organism Common	:	SNAKE
	Organism Scientific	:	BOTHROPS PIRAJAI
	Organism Taxid	:	113192
	Synonym	:	PIRATOXIN-I, PRTX-I, MYOTOXIN SIV-SP5

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:20 , LYS A:115 , ARG A:118	BINDING SITE FOR RESIDUE SO4 A 500
2	AC2	SOFTWARE	LYS A:16 , ASN A:17 , SER A:21 , HOH A:595 , HOH A:635 , HOH B:544	BINDING SITE FOR RESIDUE TRS A 501
3	AC3	SOFTWARE	LYS A:7 , HOH A:543 , GLY B:15 , LYS B:16 , ASN B:17 , LYS B:20 , SER B:21 , HOH B:646 , HOH B:659	BINDING SITE FOR RESIDUE TRS B 502

Asymmetric/Biological Unit

No.	Residues
1	A:27	-	A:126
2	A:29	-	A:45
3	A:44	-	A:105
4	A:50	-	A:133
5	A:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96
8	B:27	-	B:126
9	B:29	-	B:45
10	B:44	-	B:105
11	B:50	-	B:133
12	B:51	-	B:98
13	B:61	-	B:91
14	B:84	-	B:96

(no "Cis Peptide Bond" information available for 2Q2J)

(no "SAP(SNP)/Variant" information available for 2Q2J)

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.	PA2H1_BOTPI	43-50	2	A:44-51 B:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H2_BOTPI	43-50	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTPI	85-95	2	A:95-105 B:95-105
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H2_BOTPI	85-95	2	A:95-105 B:95-105

(no "Exon" information available for 2Q2J)

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 PA2H1_BOTPI | P58399 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 121
               SCOP domains d2q2ja_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 2q2jA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhhh...........eehhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS ----------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------PA2_ASP    -------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2j A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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 d2q2ja_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 2q2jA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhhh...........eehhhhh.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------PA2_ASP    -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2j A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H1_BOTPI | P58399 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 121
               SCOP domains d2q2jb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 2q2jB00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS ----------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------PA2_ASP    -------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2j B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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 d2q2jb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 2q2jB00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------PA2_ASP    -------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2j B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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	d2q2ja_	A:
1b	d2q2jb_	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)

Snake (Bothrops pirajai) (2)

1a	2q2jA00	A:1-133
1b	2q2jB00	B:1-133

(no "Pfam Domain" information available for 2Q2J)

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.

Chain A,B (PA2H1_BOTPI | P58399)

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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	PA2H1_BOTPI \| P58399	:	2ok9 3qnl 4yu7 4yz7
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Description

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Ligands, Modified Residues, Ions (2, 3)

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SS Bonds (14, 14)

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