2RD4 - JenaLib

Title :   DESIGN OF SPECIFIC INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOLIPASE A2 WITH PENTAPEPTIDE LEU-VAL-PHE-PHE-ALA AT 2.9 A RESOLUTION

Authors :   Z. Mirza, A. Kaur, N. Singh, M. Sinha, S. Sharma, A. Srinivasan, P. Kaur, T. P. Singh

Date :   21 Sep 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.97

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

Keywords :   Phospholipase A2, Peptide Inhibitor, Complex, Calcium, Hydrolase, Lipid Degradation, Metal-Binding, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Mirza, A. Kaur, N. Singh, M. Sinha, S. Sharma, A. Srinivasan, P. Kaur, T. P. Singh
Design Of Specific Inhibitors Of Phospholipase A2: Crystal Structure Of The Complex Of Phospholipase A2 With Pentapeptide Leu-Val-Phe-Phe-Ala At 2. 9 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJSG	50-57	1	B:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_NAJSG	50-57	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJSG	96-106	1	B:90-100
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_NAJSG	96-106	1	A:90-100

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJSG	50-57	1	B:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_NAJSG	50-57	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJSG	96-106	1	B:90-100
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_NAJSG	96-106	1	A:90-100

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJSG	50-57	0	-
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_NAJSG	50-57	0	-
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJSG	96-106	0	-
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_NAJSG	96-106	0	-

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJSG	50-57	1	B:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_NAJSG	50-57	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJSG	96-106	1	B:90-100
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_NAJSG	96-106	1	A:90-100

Exons (0, 0)

Sequences/Alignments

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:119
 aligned with PA2B1_NAJSG | P60043 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2B1_NAJSG     8 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 126
               SCOP domains d2rd4a_ A: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 2rd4A00 A:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd4 A   1 NTYQFKNMIQCTVPKRSWWDFADYGCYCGRGGSGTPIDDLDRCCQVHDNCYNSAREQGGCRPKQKTYSYECKAGTLSCSGSNNSCAATVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PA2A2_NAJSG | P60044 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    17        27        37        47        57        67        77        87        97       107       117         
          PA2A2_NAJSG     8 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 126
               SCOP domains d2rd4b_ B: Snake phospholipase A2                                                                                       SCOP domains
               CATH domains 2rd4B00 B:1-120 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh..............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd4 B   1 NRWQFKNMISCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCNPRFRTYSYECTAGTLTCTGRNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLQARCN 120
                                    10    ||  21        31        41        51        61        71        81        91       101       111         
                                         15|                                                                                                       
                                          17

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 2rd4 C   2 LVFFA   6

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 (2, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (PA2B1_NAJSG | P60043)

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 B (PA2A2_NAJSG | P60044)

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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