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(-) Description

Title :  CRYSTAL STRUCTURE OF COBRA-VENOM PHOSPHOLIPASE A2 IN A COMPLEX WITH A TRANSITION-STATE ANALOGUE
 
Authors :  S. P. White, D. L. Scott, Z. Otwinowski, P. B. Sigler
Date :  07 Sep 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. White, D. L. Scott, Z. Otwinowski, M. H. Gelb, P. B. Sigler
Crystal Structure Of Cobra-Venom Phospholipase A2 In A Complex With A Transition-State Analogue.
Science V. 250 1560 1990
PubMed-ID: 2274787
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Engineered: YES
    Organism Common: CHINESE COBRA
    Organism Scientific: NAJA ATRA
    Organism Taxid: 8656

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GEL2Ligand/Ion1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:27 , GLY A:29 , GLY A:31 , ASP A:48 , GEL A:930BINDING SITE FOR RESIDUE CA A 801
02AC2SOFTWARETYR B:27 , GLY B:29 , GLY B:31 , ASP B:48 , GEL B:935BINDING SITE FOR RESIDUE CA B 802
03AC3SOFTWARETYR A:24 , GLY A:25 , CYS A:28 , HOH A:429 , HOH A:709BINDING SITE FOR RESIDUE CA A 803
04AC4SOFTWARETYR B:24 , GLY B:25 , CYS B:28 , HOH B:481BINDING SITE FOR RESIDUE CA B 804
05AC5SOFTWARELEU A:2 , TRP A:18 , PHE A:21 , TYR A:27 , GLY A:29 , ARG A:30 , GLY A:31 , CYS A:44 , HIS A:47 , ASP A:48 , ASN A:52 , TYR A:63 , HOH A:421 , HOH A:711 , CA A:801BINDING SITE FOR RESIDUE GEL A 930
06AC6SOFTWARELEU B:2 , LYS B:6 , ILE B:9 , TRP B:18 , TYR B:27 , GLY B:29 , GLY B:31 , CYS B:44 , HIS B:47 , ASP B:48 , TYR B:51 , ASN B:52 , TYR B:63 , PHE B:64 , CA B:802BINDING SITE FOR RESIDUE GEL B 935
07CA1UNKNOWNCYS A:28 , ARG A:30 , GLY A:32 , ASN A:49NULL
08CA2UNKNOWNTYR A:24 , GLY A:25 , CYS A:28NULL
09CA3UNKNOWNCYS B:28 , ARG B:30 , GLY B:32 , ASN B:49NULL
10CA4UNKNOWNTYR B:24 , GLY B:25 , CYS B:28NULL

(-) SS Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:71
2A:26 -A:118
3A:28 -A:44
4A:43 -A:99
5A:50 -A:92
6A:60 -A:85
7A:78 -A:90
8B:11 -B:71
9B:26 -B:118
10B:28 -B:44
11B:43 -B:99
12B:50 -B:92
13B:60 -B:85

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1POB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A1_NAJAT70-77
 		  2A:43-50
B:43-50
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A1_NAJAT116-126
 		  2A:89-99
B:89-99

(-) Exons   (0, 0)

(no "Exon" information available for 1POB)

(-) 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:118
 aligned with PA2A1_NAJAT | P00598 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:118
                                    37        47        57        67        77        87        97       107       117       127       137        
          PA2A1_NAJAT    28 NLYQFKNMIQCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGGNNACAAAVCDCDRLAAICFAGAPYNNNNYNIDLKARC 145
               SCOP domains d1poba_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1pobA00 A:1-118 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhh...........eeee..eeee....hhhhhhhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1pob A   1 NLYQFKNMIQCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGGNNACAAAVCDCDRLAAICFAGAPYNDNDYNINLKARC 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2A1_NAJAT | P00598 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:118
                                    37        47        57        67        77        87        97       107       117       127       137        
          PA2A1_NAJAT    28 NLYQFKNMIQCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGGNNACAAAVCDCDRLAAICFAGAPYNNNNYNIDLKARC 145
               SCOP domains d1pobb_ B: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1pobB00 B:1-118 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhh...........eeee..eeee....hhhhhhhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1pob B   1 NLYQFKNMIQCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGGNNACAAAVCDCDRLAAICFAGAPYNDNDYNINLKARC 118
                                    10        20        30        40        50        60        70        80        90       100       110
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2A1_NAJAT | P00598)
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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  3.1.1.4
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 Related Entries

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        PA2A1_NAJAT | P00598: 1poa 2osh

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