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

(-) Description

Title :  STRUCTURAL INSIGHTS FOR FATTY ACID BINDING IN A LYS49 PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF MYOTOXIN II FROM BOTHROPS MOOJENI COMPLEXED WITH STEARIC ACID
 
Authors :  L. Watanabe, A. M. Soares, R. J. Ward, M. R. Fontes, R. K. Arni
Date :  08 Nov 04  (Deposition) - 29 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipase A2, Stearic Acid, Crystal Structure, Dimer Interface, Fatty Acid Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Watanabe, A. M. Soares, R. J. Ward, M. R. Fontes, R. K. Arni
Structural Insights For Fatty Acid Binding In A Lys49-Phospholipase A(2): Crystal Structure Of Myotoxin Ii From Bothrops Moojeni Complexed With Stearic Acid
Biochimie V. 87 161 2005
PubMed-ID: 15760708  |  Reference-DOI: 10.1016/J.BIOCHI.2004.11.005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 2
    Chains: A, B
    EC Number: 3.1.1.4
    Organism Scientific: BOTHROPS MOOJENI
    Organism Taxid: 98334
    Other Details: VENOM GLANDS
    Synonym: MYOTOXIN II, MJTX-II, M-VI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2STE6Ligand/IonSTEARIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:34 , LYS B:53BINDING SITE FOR RESIDUE SO4 B 301
02AC2SOFTWARELYS A:116 , TYR A:117 , LYS B:116 , TYR B:117BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREASN B:17 , LYS B:20BINDING SITE FOR RESIDUE SO4 B 303
04AC4SOFTWAREASN A:17 , LYS A:20BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY A:33 , ARG A:34 , LYS A:53BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWARELEU A:2 , PHE A:3 , PRO A:18 , ASN A:28 , CYS A:29 , GLY A:30 , CYS A:45 , HIS A:48 , LYS A:49 , STE A:202 , PRO B:125BINDING SITE FOR RESIDUE STE A 201
07AC7SOFTWAREGLY A:30 , VAL A:31 , LYS A:49 , TYR A:52 , LYS A:69 , STE A:201 , ALA B:19 , GLY B:23 , VAL B:31 , STE B:204BINDING SITE FOR RESIDUE STE A 202
08AC8SOFTWARETYR A:121 , TYR B:22 , ASN B:28 , CYS B:29 , GLY B:30 , CYS B:45 , HIS B:48 , LYS B:49BINDING SITE FOR RESIDUE STE B 203
09AC9SOFTWARESTE A:202 , LEU B:2 , GLY B:30 , LYS B:49 , TYR B:52 , LYS B:69BINDING SITE FOR RESIDUE STE B 204
10BC1SOFTWARELYS A:7 , LEU A:10 , GLN A:11 , TYR A:75 , TRP A:77 , GLN B:11 , GLY B:15BINDING SITE FOR RESIDUE STE A 205
11BC2SOFTWARELEU A:10 , GLN A:11 , GLY A:15 , PHE B:3 , LYS B:7 , LEU B:10 , GLN B:11 , TYR B:75 , TRP B:77BINDING SITE FOR RESIDUE STE B 206

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:127
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:90
7A:84 -A:96
8B:27 -B:127
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:90
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H2_BOTMO43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H2_BOTMO85-95
 		  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1XXS)

(-) 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:122
 aligned with PA2H2_BOTMO | Q9I834 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
          PA2H2_BOTMO     1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPFCKKADPC 122
               SCOP domains d1xxsa_ A: automated matches                                                                                               SCOP domains
               CATH domains 1xxsA00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxs A   1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPACKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        89||     100       110       120  ||   131  
                                       13|                                    53|  61|                     90|                            123|        
                                        15                                     57   67                      92                             125        


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2H2_BOTMO | Q9I834 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
          PA2H2_BOTMO     1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPFCKKADPC 122
               SCOP domains d1xxsb_ B: automated matches                                                                                               SCOP domains
               CATH domains 1xxsB00 B:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxs B   1 SLFELGKMILQETGKNPAKSYGVYGCNCGVGGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNSCLKELCECDKAVAICLRENLDTYNKKYRYNYLKPACKKADPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        89||     100       110       120  ||   131  
                                       13|                                    53|  61|                     90|                            123|        
                                        15                                     57   67                      92                             125
   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/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 1XXS)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2H2_BOTMO | Q9I834)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    STE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xxs)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  1xxs
    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
  PA2H2_BOTMO | Q9I834
    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)
  3.1.1.4
    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
  PA2H2_BOTMO | Q9I834
    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
        PA2H2_BOTMO | Q9I834: 4kf3 4yv5

(-) Related Entries Specified in the PDB File

1god LYS49-PLA2
1pa0 LYS49-PLA2: BNSP-7
1pc9 LYS49-PLA2: BNSP-6