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(-) Description

Title :  DESIGN OF SPECIFIC INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AND A DESIGNED PENTAPEPTIDE LEU-ALA-ILE-TYR-SER AT 2.0 RESOLUTION
 
Authors :  V. Chandra, J. Jasti, P. Kaur, S. Dey, C. Betzel, T. P. Singh
Date :  04 Aug 01  (Deposition) - 06 Nov 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Neurotoxic, Designed Peptide, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Chandra, J. Jasti, P. Kaur, S. Dey, A. Srinivasan, C. H. Betzel, T. P. Singh
Design Of Specific Peptide Inhibitors Of Phospholipase A2: Structure Of A Complex Formed Between Russell'S Viper Phospholipase A2 And A Designed Peptide Leu-Ala-Ile-Tyr-Ser (Laiys).
Acta Crystallogr. , Sect. D V. 58 1813 2002
PubMed-ID: 12351825  |  Reference-DOI: 10.1107/S0907444902013720
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Organism Scientific: DABOIA RUSSELLII PULCHELLA
    Organism Taxid: 97228
 
Molecule 2 - PEPTIDE INHIBITOR
    Chains: P
    Engineered: YES
    Other Details: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABP
Biological Unit 1 (1x): A P
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:131 , CYS A:133 , LYS B:69BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARELYS A:38 , TYR A:120 , HOH A:523 , HOH B:318BINDING SITE FOR RESIDUE ACY A 301
3AC3SOFTWAREARG B:107 , HOH B:366 , HOH B:437BINDING SITE FOR RESIDUE ACY B 302
4AC4SOFTWARESER B:90BINDING SITE FOR RESIDUE ACY B 303
5AC5SOFTWARELEU A:2 , LEU A:3 , PHE A:5 , GLY A:6 , LYS A:7 , LEU A:10 , ALA A:18 , ILE A:19 , TYR A:22 , TYR A:28 , CYS A:29 , GLY A:30 , TRP A:31 , CYS A:45 , HIS A:48 , ASP A:49 , HOH A:504 , HOH A:513 , VAL B:47 , ASN B:54 , CYS B:133 , HOH P:216BINDING SITE FOR CHAIN P OF PEPTIDE INHIBITOR

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:19 -Pro A:20
2Ile B:19 -Pro B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JQ8)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B8_DABRR43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B8_DABRR85-95
 		  2A:95-105
B:95-105
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B8_DABRR43-50
 		  1A:44-51
-
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B8_DABRR85-95
 		  1A:95-105
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B8_DABRR43-50
 		  1-
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B8_DABRR85-95
 		  1-
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1JQ8)

(-) 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:121
 aligned with PA2B8_DABRR | P59071 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2B8_DABRR     1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 121
               SCOP domains d1jq8a_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1jq8A00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jq8 A   1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131|
                                        14|                                      56|||                 86|                               122|    131|
                                         16                                       59||                  88                                124     133
                                                                                   61|                                                               
                                                                                    67                                                               


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2B8_DABRR | P59071 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2B8_DABRR     1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 121
               SCOP domains d1jq8b_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains 1jq8B00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jq8 B   1 SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCCYGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNLNTYSKKYMLYPDFLCKGELKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131|
                                        14|                                      56|||                 86|                               122|    131|
                                         16                                       59||                  88                                124     133
                                                                                   61|                                                               
                                                                                    67                                                               


Chain P 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
                 1jq8 P   1 LAIYS   5
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JQ8)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PA2B8_DABRR | P59071)
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.
    GO:0072556    other organism presynaptic membrane    A presynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A presynaptic membrane is specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

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  1jq8
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  PA2B8_DABRR | P59071
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  3.1.1.4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PA2B8_DABRR | P59071: 1cl5 1fb2 1fv0 1jq9 1kpm 1oxl 1oyf 1q6v 1q7a 1skg 1sqz 1sv3 1sv9 1sxk 1tdv 1tg1 1tg4 1tgm 1th6 1tj9 1tjk 1tk4 1tp2 1y38 1zr8 1zwp 1zyx 2arm 2b17 2do2 2dpz 2fnx 2g58 2gns 2o1n 2oli 2otf 2oth 2oub 2oyf 2pb8 2pmj 2pvt 2pws 2pyc 2q1p 2qhw 2qu9 2que 2qvd 2zbh 3cbi 3g8f 3h1x

(-) Related Entries Specified in the PDB File

1cl5 STRUCTURE OF DPLA2 AT 2.45
1fb2 STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 RESOLUTION
1fe7 STRUCTURE OF DPLA2 COMPLEXED WITH VITAMIN E
1fv0 STRUCTURE OF DPLA2 COMPLEXED WITH ARISTOLOCHIC ACID
1jq9 STRUCTURE OF DPLA2 COMPLEXED WITH PENTAPEPTIDE FLSYK