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Asym./Biol. Unit (Jmol Viewer)

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

Title :   PHOSPHOLIPASE ACII4 FROM AUSTRALIAN KING BROWN SNAKE

Authors :   L. W. Guddat, E. K. Millers

Date :   27 Dec 11 (Deposition) - 13 Feb 13 (Release) - 13 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.56

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

Keywords :   Wing Motif, Phospholipase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Trabi, E. -K. Millers, R. Richards, H. Snelling, R. Keegan, M. F. Lavin, J. De Jersey, L. W. Guddat, P. Masci
Mechanistic Studies On The Anticoagulant Activity Of A Phospholipase A2 From The Venom Of The Australian King Brow Snake (Pseudechis Australis)
To Be Published
PubMed: search

Molecule 1 - PHOSPHOLIPASE A2 ISOZYME PA-11
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Organism Common	:	KING BROWN SNAKE
	Organism Scientific	:	PSEUDECHIS AUSTRALIS
	Organism Taxid	:	8670
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:5 , HOH A:403 , HOH A:433 , HOH A:440	BINDING SITE FOR RESIDUE EDO A 201
02	AC2	SOFTWARE	PRO A:82 , CYS A:84 , LYS A:85 , HOH A:408 , HOH A:417 , HOH A:430	BINDING SITE FOR RESIDUE SO4 A 202
03	AC3	SOFTWARE	GLN A:4 , ASN A:7 , TRP A:69 , HOH A:400 , HOH A:401 , HOH A:402 , GLN B:4 , ASN B:7 , TRP B:69	BINDING SITE FOR RESIDUE SO4 A 203
04	AC4	SOFTWARE	SER A:16 , ARG A:17 , TYR A:104 , LYS A:115	BINDING SITE FOR RESIDUE SO4 A 204
05	AC5	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:440 , HOH A:468	BINDING SITE FOR RESIDUE CA A 205
06	AC6	SOFTWARE	TRP A:31 , LYS A:63 , HOH A:403 , CYS B:60	BINDING SITE FOR RESIDUE PEG A 206
07	AC7	SOFTWARE	PRO B:82 , GLY B:83 , CYS B:84 , LYS B:85 , HOH B:356 , HOH B:458	BINDING SITE FOR RESIDUE SO4 B 201
08	AC8	SOFTWARE	TYR B:28 , GLY B:30 , GLY B:32 , ASP B:49 , HOH B:459 , HOH B:460	BINDING SITE FOR RESIDUE CA B 202
09	AC9	SOFTWARE	TYR B:22 , HOH B:371 , HOH B:460	BINDING SITE FOR RESIDUE PEG B 203
10	BC1	SOFTWARE	GLY A:56 , CYS A:60 , TRP B:31 , LYS B:63 , HOH B:402	BINDING SITE FOR RESIDUE PEG B 204

Asymmetric/Biological Unit

No.	Residues
1	A:11	-	A:71
2	A:27	-	A:117
3	A:29	-	A:45
4	A:44	-	A:98
5	A:51	-	A:91
6	A:60	-	A:84
7	A:78	-	A:89
8	B:11	-	B:71
9	B:27	-	B:117
10	B:29	-	B:45
11	B:44	-	B:98
12	B:51	-	B:91
13	B:60	-	B:84
14	B:78	-	B:89

(no "Cis Peptide Bond" information available for 3V9M)

(no "SAP(SNP)/Variant" information available for 3V9M)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BB_PSEAU	44-51	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BB_PSEAU	88-98	2	A:88-98 B:88-98

(no "Exon" information available for 3V9M)

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:118
 aligned with PA2BB_PSEAU | P04056 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
          PA2BB_PSEAU     1 NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK 118
               SCOP domains d3v9ma_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS ------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3v9m A   1 NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK 118
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2BB_PSEAU | P04056 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
          PA2BB_PSEAU     1 NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK 118
               SCOP domains d3v9mb_ B: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eeee..eeee...hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS ------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3v9m B   1 NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK 118
                                    10        20        30        40        50        60        70        80        90       100       110

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)

Pseudechis australis [TaxId: 8670] (1)

1a	d3v9ma_	A:
1b	d3v9mb_	B:

(no "CATH Domain" information available for 3V9M)

(no "Pfam Domain" information available for 3V9M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2BB_PSEAU | P04056)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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