2QOG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CROTOXIN B, THE BASIC PLA2 FROM CROTALUS DURISSUS TERRIFICUS.

Authors :   D. P. Marchi-Salvador, L. C. Correa, M. R. M. Fontes

Date :   20 Jul 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Crotoxin B Cd-Cdt Basic-Pla2, Calcium, Hydrolase, Lipid Degradation, Metal-Binding, Secreted, Neurotoxin, Presynaptic Neurotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. P. Marchi-Salvador, L. C. Correa, A. J. Magro, C. Z. Oliveira, A. M. Soares, M. R. Fontes
Insights Into The Role Of Oligomeric State On The Biological Activities Of Crotoxin: Crystal Structure Of A Tetrameric Phospholipase A2 Formed By Two Isoforms Of Crotoxin B From Crotalus Durissus Terrificus Venom.
Proteins V. 72 883 2008
PubMed-ID: 18275084 | Reference-DOI: 10.1002/PROT.21980
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2 CB2
	Chains	:	A, D
	EC Number	:	3.1.1.4
	Organism Common	:	TROPICAL RATTLESNAKE
	Organism Scientific	:	CROTALUS DURISSUS TERRIFICUS
	Organism Taxid	:	8732
	Other Details	:	VENOM GLANDS
	Strain	:	TERRIFICUS
	Synonym	:	CROTOXIN BASIC CHAIN 2, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE

Molecule 2 - PHOSPHOLIPASE A2 CB1
	Chains	:	B, C
	EC Number	:	3.1.1.4
	Organism Common	:	TROPICAL RATTLESNAKE
	Organism Scientific	:	CROTALUS DURISSUS TERRIFICUS
	Organism Taxid	:	8732
	Other Details	:	VENOM GLANDS
	Strain	:	TERRIFICUS
	Synonym	:	CROTOXIN BASIC CHAIN 1, PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49	BINDING SITE FOR RESIDUE CA B 134
2	AC2	SOFTWARE	TYR C:28 , GLY C:30 , GLY C:32 , ASP C:49	BINDING SITE FOR RESIDUE CA C 134

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
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/Biological Unit

No.	Residues
1	Val A:19	-	Pro A:20
2	Ile B:19	-	Pro B:20
3	Ile C:19	-	Pro C:20
4	Val D:19	-	Pro D:20

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BA_CRODU	59-66	2	A:44-51 D:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BC_CRODU	59-66	2	B:44-51 C:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BA_CRODU	101-111	2	A:95-105 D:95-105
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BC_CRODU	101-111	2	B:95-105 C:95-105

(no "Exon" information available for 2QOG)

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:122
 aligned with PA2BA_CRODU | P24027 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BA_CRODU    17 SLLQFNKMIKFETRKNAVPFYAFYGCYCGWGGQGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYRYSLKSGYITCGKGTWCKEQICECDRVAAECLRRSLSTYKNEYMFYPDSRCREPSETC 138
               SCOP domains d2qoga_ A: automated matches                                                                                               SCOP domains
               CATH domains 2qogA00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhhhhhhh.......eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS ------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qog A   1 SLLQFNKMIKFETRKNAVPFYAFYGCYCGWGGQGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYRYSLKSGYITCGKGTWCKEQICECDRVAAECLRRSLSTYKNEYMFYPDSRCREPSETC 133
                                    10   ||   21        31        41        51    ||||69        79    ||  90       100       110       120 ||    131  
                                        14|                                      56|||               84|                                 122|         
                                         16                                       59||                86                                  124         
                                                                                   61|                                                                
                                                                                    67

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2BC_CRODU | P62022 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BC_CRODU    17 HLLQFNKMIKFETRKNAIPFYAFYGCYCGWGGRGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYPYSLKSGYITCGKGTWCEEQICECDRVAAECLRRSLSTYKYGYMFYPDSRCRGPSETC 138
               SCOP domains d2qogb_ B: automated matches                                                                                               SCOP domains
               CATH domains 2qogB00 B:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............ee......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS ------------------------------------------------------------------------ PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE (1)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qog B   1 HLLQFNKMIKFETRKNAIPFYAFYGCYCGWGGRGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYPYSLKSGYITCGKGTWCEEQICECDRVAAECLRRSLSTYKYGYMFYPDSRCRGPSETC 133
                                    10   ||   21        31        41        51    ||||69        79    ||  90       100       110       120 ||    131  
                                        14|                                      56|||               84|                                 122|         
                                         16                                       59||                86                                  124         
                                                                                   61|                                                                
                                                                                    67

Chain C from PDB  Type:PROTEIN  Length:122
 aligned with PA2BC_CRODU | P62022 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BC_CRODU    17 HLLQFNKMIKFETRKNAIPFYAFYGCYCGWGGRGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYPYSLKSGYITCGKGTWCEEQICECDRVAAECLRRSLSTYKYGYMFYPDSRCRGPSETC 138
               SCOP domains d2qogc_ C: automated matches                                                                                               SCOP domains
               CATH domains 2qogC00 C:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............ee......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS ------------------------------------------------------------------------ PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE (1)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qog C   1 HLLQFNKMIKFETRKNAIPFYAFYGCYCGWGGRGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYPYSLKSGYITCGKGTWCEEQICECDRVAAECLRRSLSTYKYGYMFYPDSRCRGPSETC 133
                                    10   ||   21        31        41        51    ||||69        79    ||  90       100       110       120 ||    131  
                                        14|                                      56|||               84|                                 122|         
                                         16                                       59||                86                                  124         
                                                                                   61|                                                                
                                                                                    67

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with PA2BA_CRODU | P24027 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BA_CRODU    17 SLLQFNKMIKFETRKNAVPFYAFYGCYCGWGGQGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYRYSLKSGYITCGKGTWCKEQICECDRVAAECLRRSLSTYKNEYMFYPDSRCREPSETC 138
               SCOP domains d2qogd_ D: automated matches                                                                                               SCOP domains
               CATH domains 2qogD00 D:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh.hhhhhh.....eeee..eeee...hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS ------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qog D   1 SLLQFNKMIKFETRKNAVPFYAFYGCYCGWGGQGRPKDATDRCCFVHDCCYGKLAKCNTKWDIYRYSLKSGYITCGKGTWCKEQICECDRVAAECLRRSLSTYKNEYMFYPDSRCREPSETC 133
                                    10   ||   21        31        41        51    ||||69        79    ||  90       100       110       120 ||    131  
                                        14|                                      56|||               84|                                 122|         
                                         16                                       59||                86                                  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 '\|'

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: automated matches (75)

Crotalus durissus [TaxId: 8732] (2)

1a	d2qoga_	A:
1b	d2qogb_	B:
1c	d2qogc_	C:
1d	d2qogd_	D:

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)

Tropical rattlesnake (Crotalus durissus terrificus) (1)

1a	2qogA00	A:1-133
1b	2qogD00	D:1-133
1c	2qogB00	B:1-133
1d	2qogC00	C:1-133

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,D (PA2BA_CRODU | P24027)

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.
	GO:0072556	other organism presynaptic membrane	A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

Chain B,C (PA2BC_CRODU | P62022)

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.
	GO:0072556	other organism presynaptic membrane	A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

Asymmetric/Biological Unit
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		Val A:19 - Pro A:20	[ RasMol ]
		Val D:19 - Pro D:20	[ RasMol ]

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	2qog
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	PA2BA_CRODU \| P24027
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	PA2BC_CRODU \| P62022
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	PA2BC_CRODU \| P62022	:	3r0l

2ok9	LYS49-PLA2 (PRTX-I-BPB) FROM BOTHROPS PIRAJAI
2oqd	ASP49-PLA2 (BTHTX-II) FROM BOTHROPS JARARACUSSU

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (28, 28)

Cis Peptide Bonds (4, 4)

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