1PC9 - JenaLib

Title :   CRYSTAL STRUCTURE OF BNSP-6, A LYS49-PHOSPHOLIPASE A2

Authors :   A. J. Magro, A. M. Soares, J. R. Giglio, M. R. M. Fontes

Date :   16 May 03 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Lys49-Phospholipase A2, Myotoxin, Crystal Structure, Bothrops, Venom. , Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Magro, A. M. Soares, J. R. Giglio, M. R. M. Fontes
Crystal Structures Of Bnsp-7 And Bnsp-6, Two Lys49-Phospholipases A(2): Quaternary Structure And Inhibition Mechanism Insights.
Biochem. Biophys. Res. Commun. V. 311 713 2003
PubMed-ID: 14623331 | Reference-DOI: 10.1016/J.BBRC.2003.10.047
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	A/B	G	36	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	A	G	36	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	B	G	36	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	2	A:95-105 B:95-105

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	1	A:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	1	A:95-105 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	1	- B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	1	- B:95-105

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
	(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 PA2H_BOTPA | Q9IAT9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           PA2H_BOTPA     - -SFELGKMILQETGKNPAKSYGAYGCNCGVLGRGQPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 120
               SCOP domains d1pc9a_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1pc9A00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------G-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pc9 A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGGPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 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 PA2H_BOTPA | Q9IAT9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           PA2H_BOTPA     - -SFELGKMILQETGKNPAKSYGAYGCNCGVLGRGQPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 120
               SCOP domains d1pc9b_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1pc9B00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------G-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pc9 B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGGPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2H_BOTPA | Q9IAT9)

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:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pc9)

	Sites
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pc9)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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