3JR8 - JenaLib

Title :   CRYSTAL STRUCTURE OF BTHTX-II (ASP49-PLA2 FROM BOTHROPS JARARACUSSU SNAKE VENOM) WITH CALCIUM IONS

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

Date :   08 Sep 09 (Deposition) - 08 Sep 10 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Phospholipases A2, Asp49-Pla2, Miotoxic Asp49-Pla2, Bothropstoxin Ii, Bthtx-Ii, Disulfide Bond, Hydrolase, Lipid Degradation, Metal- Binding, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Dos Santos, M. Cintra-Francischinelli, R. J. Borges, C. A. Fernandes, P. Pizzo, A. C. Cintra, A. S. Braz, A. M. Soares, M. R. Fontes
Structural, Functional, And Bioinformatics Studies Reveal A New Snake Venom Homologue Phospholipase A2 Class.
Proteins V. 79 61 2011
PubMed-ID: 20878713 | Reference-DOI: 10.1002/PROT.22858

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (14, 14)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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.	PA2B2_BOTJR	59-66	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B2_BOTJR	101-111	2	A:95-105 B:95-105

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.	PA2B2_BOTJR	59-66	2	A:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B2_BOTJR	101-111	2	A:95-105 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B2_BOTJR	59-66	2	- B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B2_BOTJR	101-111	2	- 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:122
 aligned with PA2B2_BOTJR | P45881 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2B2_BOTJR    17 DLWQFGQMILKETGKLPFPYYTTYGCYCGWGGQGQPKDATDRCCFVHDCCYGKLTNCKPKTDRYSYSRENGVIICGEGTPCEKQICECDKAAAVCFRENLRTYKKRYMAYPDVLCKKPAEKC 138
               SCOP domains d3jr8a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............ee......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr8 A   1 DLWQFGQMILKETGKLPFPYYTTYGCYCGWGGQGQPKDATDRCCFVHDCCYGKLTNCKPKTDRYSYSRENGVIICGEGTPCEKQICECDKAAAVCFRENLRTYKKRYMAYPDVLCKKPAEKC 133
                                    10   ||   21        31        41        51    ||||69        79        90       100       110       120 ||    131  
                                        14|                                      56|||                   88|                             122|         
                                         16                                       59||                    90                              124         
                                                                                   61|                                                                
                                                                                    67

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2B2_BOTJR | P45881 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2B2_BOTJR    17 DLWQFGQMILKETGKLPFPYYTTYGCYCGWGGQGQPKDATDRCCFVHDCCYGKLTNCKPKTDRYSYSRENGVIICGEGTPCEKQICECDKAAAVCFRENLRTYKKRYMAYPDVLCKKPAEKC 138
               SCOP domains d3jr8b_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Phospholip_A2_1-3jr8B01 B:1-133                                                                                            Pfam domains (1)
           Pfam domains (2) Phospholip_A2_1-3jr8B02 B:1-133                                                                                            Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhh............ee......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr8 B   1 DLWQFGQMILKETGKLPFPYYTTYGCYCGWGGQGQPKDATDRCCFVHDCCYGKLTNCKPKTDRYSYSRENGVIICGEGTPCEKQICECDKAAAVCFRENLRTYKKRYMAYPDVLCKKPAEKC 133
                                    10   ||   21        31        41        51    ||||69        79        90       100       110       120 ||    131  
                                        14|                                      56|||                   88|                             122|         
                                         16                                       59||                    90                              124         
                                                                                   61|                                                                
                                                                                    67

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 (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2B2_BOTJR | P45881)

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.

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