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Description

Title :   CRYSTALLOGRAPHIC REFINEMENT OF BOVINE PRO-PHOSPHOLIPASE A2 AT 1.6 ANGSTROMS RESOLUTION

Authors :   B. C. Finzel, P. C. Weber, D. H. Ohlendorf, F. R. Salemme

Date :   07 Sep 90 (Deposition) - 15 Oct 91 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Carboxylic Ester Hydrolase Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. C. Finzel, P. C. Weber, D. H. Ohlendorf, F. R. Salemme
Crystallographic Refinement Of Bovine Pro-Phospholipase A2 At 1. 6 A Resolution.
Acta Crystallogr. , Sect. B V. 47 814 1991
PubMed-ID: 1793547 | Reference-DOI: 10.1107/S0108768191004226
(for further references see the PDB file header)

Compounds

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 3)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:315 , HOH A:316	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	LEU A:2 , PHE A:5 , LEU A:19 , PHE A:106 , HOH A:361	BINDING SITE FOR RESIDUE MPD A 301
3	AC3	SOFTWARE	LEU A:19 , HOH A:332	BINDING SITE FOR RESIDUE MPD A 302
4	CA1	UNKNOWN	TYR A:28 , CYS A:29 , GLY A:30 , LEU A:31 , GLY A:32 , ASP A:49 , CA A:201	NULL

SS Bonds (7, 7)

Asymmetric/Biological Unit

No.	Residues
1	A:11	-	A:77
2	A:27	-	A:123
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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 4BP2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 4BP2)

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_BOVIN	66-73	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_BOVIN	117-127	1	A:95-105

Exons (0, 0)

(no "Exon" information available for 4BP2)

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
	(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:117
 aligned with PA21B_BOVIN | P00593 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
          PA21B_BOVIN    23 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 145
               SCOP domains d4bp2a_ A: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 4bp2A00 A:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhhh......------....eeee..eeee....hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bp2 A   1 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVL------NNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 123
                                    10        20        30        40        50        60   |     -|       80        90       100       110       120   
                                                                                          64     71

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)

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: Phospholipase A2 (72)

Cow (Bos taurus), pancreas [TaxId: 9913] (32)

d4bp2a_

CATH Domains (1, 1)

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)

Cattle (Bos taurus) (29)

4bp2A00

A:1-123

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 4BP2)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PA21B_BOVIN | P00593)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bp2)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PA21B_BOVIN \| P00593	:	1bp2 1bpq 1bvm 1c74 1ceh 1fdk 1g4i 1gh4 1irb 1kvw 1kvx 1kvy 1mks 1mkt 1mku 1mkv 1o2e 1o3w 1une 1vkq 1vl9 2b96 2bax 2bch 2bd1 2bp2 2bpp 2zp3 2zp4 2zp5 3bp2

Related Entries Specified in the PDB File

2bp2	PRELIMINARY MODEL