3CXI - JenaLib

Title :   STRUCTURE OF BTHTX-I COMPLEXED WITH ALPHA-TOCOPHEROL

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

Date :   24 Apr 08 (Deposition) - 05 May 09 (Release) - 28 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

Keywords :   Myotoxin, Bothrops Jaracussu, Lys49-Pla2, Snake Venom, Phospholipase A2, X-Ray Crystallography, Secreted (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)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	unknown	LYS A:16 , LYS A:20 , LYS A:115 , ARG A:118	BINDING SITE FOR RESIDUE SO4 A 303
02	AC2	unknown	THR A:81 , ILE A:104 , ARG A:107 , LYS B:36	BINDING SITE FOR RESIDUE SO4 A 305
03	AC3	unknown	LYS B:20 , THR B:59 , LYS B:115 , ARG B:118	BINDING SITE FOR RESIDUE SO4 B 308
04	AC4	unknown	GLY B:15 , LYS B:16 , ASN B:17 , LYS B:20 , PRO B:90	BINDING SITE FOR RESIDUE SO4 B 309
05	AC5	unknown	PHE A:125 , LYS B:7 , LEU B:10 , GLN B:11 , TYR B:75 , TRP B:77	BINDING SITE FOR RESIDUE PE4 B 310
06	AC6	unknown	LEU A:32 , PRO A:123 , LEU B:2 , PHE B:3 , LEU B:5 , GLY B:6 , LYS B:7 , ILE B:9 , PRO B:18 , TYR B:22 , CYS B:29 , GLY B:30 , HIS B:48 , LYS B:49 , TYR B:52	BINDING SITE FOR RESIDUE VIT B 311
07	AC7	unknown	LEU A:2 , PHE A:3 , LEU A:5 , GLY A:6 , ASN A:17 , PRO A:18 , ALA A:19 , TYR A:22 , GLY A:23 , GLY A:30 , TYR A:52 , LEU B:121	BINDING SITE FOR RESIDUE VIT A 306
08	AC8	SOFTWARE	LYS A:16 , LYS A:20 , LYS A:115 , ARG A:118	BINDING SITE FOR RESIDUE SO4 A 303
09	AC9	SOFTWARE	THR A:81 , ILE A:104 , ARG A:107 , HOH A:313 , HOH A:316 , LYS B:36	BINDING SITE FOR RESIDUE SO4 A 305
10	AD1	SOFTWARE	LYS B:20 , THR B:59 , LYS B:115 , ARG B:118 , SO4 B:309	BINDING SITE FOR RESIDUE SO4 B 308
11	AD2	SOFTWARE	GLY B:15 , LYS B:16 , ASN B:17 , LYS B:20 , PRO B:90 , SO4 B:308 , HOH B:430 , HOH B:469	BINDING SITE FOR RESIDUE SO4 B 309
12	AD3	SOFTWARE	LEU A:2 , PHE A:3 , LEU A:5 , GLY A:6 , ASN A:17 , PRO A:18 , ALA A:19 , TYR A:22 , GLY A:23 , GLY A:30 , VAL A:31 , TYR A:52 , HOH A:336 , LEU B:121	BINDING SITE FOR RESIDUE VIT A 306
13	AD4	SOFTWARE	PHE A:125 , LYS B:7 , LEU B:10 , GLN B:11 , TYR B:75 , TRP B:77 , VIT B:311 , HOH B:495 , HOH B:499	BINDING SITE FOR RESIDUE PE4 B 310
14	AD5	SOFTWARE	VAL A:31 , LEU A:32 , PRO A:123 , LEU B:2 , PHE B:3 , LEU B:5 , GLY B:6 , LYS B:7 , ILE B:9 , PRO B:18 , TYR B:22 , CYS B:29 , GLY B:30 , HIS B:48 , LYS B:49 , TYR B:52 , PE4 B:310 , HOH B:484	BINDING SITE FOR RESIDUE VIT B 311

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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 PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d3cxia_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3cxiA00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cxi A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 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 PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d3cxib_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 3cxiB00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cxi B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 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)
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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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2B1_BOTJR | Q90249)

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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	3cxi
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