3T0R - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MJTX-I, A MYOTOXIC LYS49-PHOSPHOLIPASE A2 FROM BOTHROPS MOOJENI

Authors :   G. H. M. Salvador, D. P. Marchi-Salvador, M. R. M. Fontes

Date :   20 Jul 11 (Deposition) - 01 Aug 12 (Release) - 01 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: C  (1x)
Biol. Unit 6: D  (1x)

Keywords :   Lys49-Phospholipase A2, Myotoxin, Venom Glands, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. H. M. Salvador, D. P. Marchi-Salvador, M. R. M. Fontes
Crystal Structure Of Mjtx-I, A Myotoxic Lys49-Phospholipase A2 From Bothrops Moojeni
To Be Published
PubMed: search

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 1
	Chains	:	A, B, C, D
	EC Number	:	3.1.1.4
	Organism Common	:	LANCE-HEADED VIPER
	Organism Scientific	:	BOTHROPS MOOJENI
	Organism Taxid	:	98334
	Synonym	:	MJTX-I, MYOTOXIN I

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B
Biological Unit 5 (1x)	:			C
Biological Unit 6 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:7 , LEU A:10 , GLN A:11 , GLY A:15 , TYR A:75 , HOH A:145 , LYS B:7 , LEU B:10 , GLN B:11 , TYR B:75	BINDING SITE FOR RESIDUE PE4 A 134

Asymmetric 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
15	C:27	-	C:126
16	C:29	-	C:45
17	C:44	-	C:105
18	C:50	-	C:133
19	C:51	-	C:98
20	C:61	-	C:91
21	C:84	-	C:96
22	D:27	-	D:126
23	D:29	-	D:45
24	D:44	-	D:105
25	D:50	-	D:133
26	D:51	-	D:98
27	D:61	-	D:91
28	D:84	-	D:96

Asymmetric Unit

No.	Residues
1	Glu C:87	-	Asn C:88
2	Cys D:84	-	Gly D:85
3	Pro D:90	-	Cys D:91

(no "SAP(SNP)/Variant" information available for 3T0R)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H1_BOTMO	43-50	4	A:44-51 B:44-51 C:44-51 D:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	4	A:95-105 B:95-105 C:95-105 D: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.	PA2H1_BOTMO	43-50	2	A:44-51 B:44-51 - -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	2	A:95-105 B: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.	PA2H1_BOTMO	43-50	2	- - C:44-51 D:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	2	- - C:95-105 D:95-105

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H1_BOTMO	43-50	1	A:44-51 - - -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	1	A:95-105 - - -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H1_BOTMO	43-50	1	- B:44-51 - -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	1	- B:95-105 - -

Biological Unit 5 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H1_BOTMO	43-50	1	- - C:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	1	- - C:95-105 -

Biological Unit 6 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H1_BOTMO	43-50	1	- - - D:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTMO	85-95	1	- - - D:95-105

(no "Exon" information available for 3T0R)

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 PA2H1_BOTMO | P82114 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTMO     1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 121
               SCOP domains d3t0ra_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0r A   1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 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_BOTMO | P82114 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTMO     1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 121
               SCOP domains d3t0rb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0r B   1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 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 C from PDB  Type:PROTEIN  Length:117
 aligned with PA2H1_BOTMO | P82114 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTMO     1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 121
               SCOP domains d3t0rc_ C: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhh..............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhh......----......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0r C   1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRD----PFCDKGRDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       | -  || ||132 
                                       13|                                    53|  61|                   88|                         118  123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

Chain D from PDB  Type:PROTEIN  Length:116
 aligned with PA2H1_BOTMO | P82114 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTMO     1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKRDVYLKPFCDKGRDC 121
               SCOP domains d3t0rd_ D: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh.............eee..eee......hhhhhhhhhhhhhhhhhhhhhhh....-----......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t0r D   1 SLVELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTNCDPKKDRYSYDWKNKTIVCGEENPCLKQLCECDKAVAICLRENKGTYNKKR-----PFCDKGRDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110      |  -  || ||132 
                                       13|                                    53|  61|                   88|                        117   123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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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 '\|'

Asymmetric Unit

Classes(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Phospholipase A2, PLA2 (282)

Superfamily: Phospholipase A2, PLA2 (282)

Family: Vertebrate phospholipase A2 (271)

Protein domain: automated matches (75)

Bothrops moojeni [TaxId: 98334] (3)

1a	d3t0ra_	A:
1b	d3t0rb_	B:
1c	d3t0rc_	C:
1d	d3t0rd_	D:

(no "CATH Domain" information available for 3T0R)

(no "Pfam Domain" information available for 3T0R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PA2H1_BOTMO | P82114)

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 Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Cys D:84 - Gly D:85	[ RasMol ]
		Glu C:87 - Asn C:88	[ RasMol ]
		Pro D:90 - Cys D:91	[ RasMol ]

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1pa0	CRYSTAL STRUCTURE OF BNSP-7, A LYS49-PLA2 FROM BOTHROPS NEUWIEDI PAULOENSIS.
2q2j	CRYSTAL STRUCTURE OF PRTX-I, A LYS49-PLA2 HOMOLOGUE FROM BOTHROPS PIRAJAI
3i3h	CRYSTAL STRUCTURE OF BTHTX-I, A LYS49-PLA2 HOMOLOGUE FROM BOTHROPS JARARACUSSU

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