Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN
 
Authors :  Y. D. Devedjiev, A. N. Popov
Date :  17 Dec 96  (Deposition) - 24 Dec 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phospholipase A2 Inhibitor, Recognition, Molecular Evolution, Neurotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Devedjiev, A. Popov, B. Atanasov, H. D. Bartunik
X-Ray Structure At 1. 76 A Resolution Of A Polypeptide Phospholipase A2 Inhibitor.
J. Mol. Biol. V. 266 160 1997
PubMed-ID: 9054978  |  Reference-DOI: 10.1006/JMBI.1996.0778
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 INHIBITOR
    Chains: A
    Organ: VENOM GLAND
    Organism Common: SAND VIPER
    Organism Scientific: VIPERA AMMODYTES
    Organism Taxid: 8704

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VPI)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1RSUNKNOWNPHE A:3 , TRP A:31 , TYR A:119RECOGNITION SITE.

(-) SS Bonds  (7, 7)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95  1A:95-105
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_VIPAE85-95  2A:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1VPI)

(-) 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:122
 aligned with PA2A_VIPAE | P04084 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           PA2A_VIPAE     1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRVNDCNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 122
               SCOP domains d1vpia_ A: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1vpiA00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........................hhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpi A   1 NLFQFGDMILQKTGKEAVHSYAIYGCYCGWGGQGRAQDATDRCCFAQDCCYGRVNDCNPKTATYTYSFENGDIVCGDNDLCLRAVCECDRAAAICLGENVNTYDKNYEYYSISHCTEESEQC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   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)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (PA2A_VIPAE | P04084)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
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:0035792    other organism postsynaptic membrane    A postsynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A postsynaptic membrane is a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters transmit the signal across the synaptic cleft to the postsynaptic membrane.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1vpi)
 
  Sites
    RS  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vpi)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vpi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PA2A_VIPAE | P04084
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PA2A_VIPAE | P04084
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PA2A_VIPAE | P04084: 1aok 1jlt 1q5t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VPI)