1GP7 - JenaLib

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Title :   ACIDIC PHOSPHOLIPASE A2 FROM VENOM OF OPHIOPHAGUS HANNAH

Authors :   H. Zhang, Z. Lin

Date :   30 Oct 01 (Deposition) - 31 Oct 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Phospholipase A2, Snake Venom, King Cobra, Cardiotoxic Activity, Myotoxic Activity, Pancreatic Loop, Crystal Structure, Hydrolase, Lipid Degradation, Calcium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhang, S. Xu, Q. Wang, S. Song, Y. Shu, Z. Lin
Structure Of A Cardiotoxic Phospholipase A(2) From Ophiophagus Hannah With The "Pancreatic Loop"
J. Struct. Biol. V. 138 207 2002
PubMed-ID: 12217659 | Reference-DOI: 10.1016/S1047-8477(02)00022-9
(for further references see the PDB file header)

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A, B, C
	EC Number	:	3.1.1.4
	Organism Common	:	KING COBRA
	Organism Scientific	:	OPHIOPHAGUS HANNAH
	Organism Taxid	:	8665
	Other Details	:	SNAKE VENOM
	Synonym	:	OHV A-PLA2, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE
	Tissue	:	VENOM

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:2008	BINDING SITE FOR RESIDUE CA A1125
2	AC2	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49	BINDING SITE FOR RESIDUE CA B1125
3	AC3	SOFTWARE	TYR C:28 , GLY C:30 , GLY C:32 , ASP C:49	BINDING SITE FOR RESIDUE CA C1125

Asymmetric Unit

No.	Residues
1	A:11	-	A:77
2	A:27	-	A:124
3	A:29	-	A:45
4	A:44	-	A:105
5	A:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96
8	B:11	-	B:77
9	B:27	-	B:124
10	B:29	-	B:45
11	B:44	-	B:105
12	B:51	-	B:98
13	B:61	-	B:91
14	B:84	-	B:96
15	C:11	-	C:77
16	C:27	-	C:124
17	C:29	-	C:45
18	C:44	-	C:105
19	C:51	-	C:98
20	C:61	-	C:91
21	C:84	-	C:96

(no "Cis Peptide Bond" information available for 1GP7)

(no "SAP(SNP)/Variant" information available for 1GP7)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A1_OPHHA	71-78	3	A:44-51 B:44-51 C:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A1_OPHHA	122-132	3	A:95-105 B:95-105 C: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.	PA2A1_OPHHA	71-78	1	A:44-51 - -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A1_OPHHA	122-132	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.	PA2A1_OPHHA	71-78	1	- B:44-51 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A1_OPHHA	122-132	1	- B: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.	PA2A1_OPHHA	71-78	1	- - C:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A1_OPHHA	122-132	1	- - C:95-105

(no "Exon" information available for 1GP7)

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:124
 aligned with PA2A1_OPHHA | P80966 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:124
                                    37        47        57        67        77        87        97       107       117       127       137       147    
          PA2A1_OPHHA    28 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 151
               SCOP domains d1gp7a_ A: Snake phospholipase A2                                                                                            SCOP domains
               CATH domains 1gp7A00 A:1-124 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gp7 A   1 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with PA2A1_OPHHA | P80966 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:124
                                    37        47        57        67        77        87        97       107       117       127       137       147    
          PA2A1_OPHHA    28 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 151
               SCOP domains d1gp7b_ B: Snake phospholipase A2                                                                                            SCOP domains
               CATH domains 1gp7B00 B:1-124 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gp7 B   1 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:124
 aligned with PA2A1_OPHHA | P80966 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:124
                                    37        47        57        67        77        87        97       107       117       127       137       147    
          PA2A1_OPHHA    28 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 151
               SCOP domains d1gp7c_ C: Snake phospholipase A2                                                                                            SCOP domains
               CATH domains 1gp7C00 C:1-124 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gp7 C   1 HLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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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Folds(

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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: Snake phospholipase A2 (124)

King cobra (Ophiophagus hannah) [TaxId: 8665] (1)

1a	d1gp7a_	A:
1b	d1gp7b_	B:
1c	d1gp7c_	C:

Asymmetric 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)

King cobra (Ophiophagus hannah) (2)

1a	1gp7A00	A:1-124
1b	1gp7B00	B:1-124
1c	1gp7C00	C:1-124

(no "Pfam Domain" information available for 1GP7)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PA2A1_OPHHA | P80966)

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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