1M8S - JenaLib

Title :   CRYSTAL STRUCTURES OF CADMIUM-BINDING ACIDIC PHOSPHOLIPASE A2 FROM THE VENOM OF AGKISTRODON HALYS PALLAS AT 1.9 RESOLUTION (CRYSTAL GROWN AT PH 5.9)

Authors :   S. Xu, L. Gu, Y. Zhou, Z. Lin

Date :   25 Jul 02 (Deposition) - 11 Feb 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Phopholipase A2-Metal Cation Complex, Three Alpha, Two Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Xu, L. Gu, T. Jiang, Y. Zhou, Z. Lin
Structures Of Cadmium-Binding Acidic Phospholipase A(2) From The Venom Of Agkistrodon Halys Pallas At 1. 9A Resolutio
Biochem. Biophys. Res. Commun. V. 300 271 2003
PubMed-ID: 12504079 | Reference-DOI: 10.1016/S0006-291X(02)02833-4
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (7, 7)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

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
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Chain A from PDB  Type:PROTEIN  Length:124
 aligned with PA2A7_GLOHA | O42191 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
          PA2A7_GLOHA     1 SLLQFETLIMKVAKKSGMVWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDPCKKEICECDRAAAICFRDNLNTYNDKKYWAFGAKNCPQEESEPC 124
               SCOP domains d1m8sa_ A: Snake phospholipase A2                                                                                            SCOP domains
               CATH domains 1m8sA00 A:1-134 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS -------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------PA2_ASP    ----------------------------- PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m8s A   1 SLVQFETLIMKVAKKSGMQWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDPCKKEICECDRAAAICFRDNLNTYNDKKYWAFGAKNCPQEESEPC 134
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120       130    
                                        14|                                      56|||                 86|                                              
                                         16                                       59||                  88                                              
                                                                                   61|                                                                  
                                                                                    67

Chain A from PDB  Type:PROTEIN  Length:124
 aligned with PA2A_GLOHA | P14418 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           PA2A_GLOHA     1 SLIQFETLIMKVAKKSGMFWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDPCKKEICECDRAAAICFRDNLTLYNDKKYWAFGAKNCPQEESEPC 124
               SCOP domains d1m8sa_ A: Snake phospholipase A2                                                                                            SCOP domains
               CATH domains 1m8sA00 A:1-134 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------PA2_HIS -------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------PA2_ASP    ----------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m8s A   1 SLVQFETLIMKVAKKSGMQWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDPCKKEICECDRAAAICFRDNLNTYNDKKYWAFGAKNCPQEESEPC 134
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120       130    
                                        14|                                      56|||                 86|                                              
                                         16                                       59||                  88                                              
                                                                                   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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PA2A7_GLOHA | O42191)

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.

Chain A (PA2A_GLOHA | P14418)

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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