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 :  CRYSTAL STRUCTURE OF ADTX1 (RHO-DA1A) FROM EASTERN GREEN MAMBA (DENDROASPIS ANGUSTICEPS)
 
Authors :  E. A. Stura, L. Vera, A. A. Maiga, C. Marchetti, A. Lorphelin, L. Bellang D. Servant, N. Gilles
Date :  28 Jan 13  (Deposition) - 08 May 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Snake Three-Finger Toxin Family, Type A Muscarinic Toxin Subfamily, Allosteric Antagonist Of The Alpha-1A Adrenergic Receptor (Adra1A), Acts As A Relaxant Of Smooth Muscle, Alpha-1A Adrenergic Receptor, G-Rhoda1A K34A, Expressed By The Venom Gland, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Maiga, L. Vera, C. Marchetti, A. Lorphelin, L. Bellanger, G. Mourier, D. Servent, N. Gilles, E. A. Stura
Crystallization Of Recombinant Green Mamba Rho-Da1A Toxin During A Lyophilization Procedure And Its Structure Determination.
Acta Crystallogr. , Sect. F V. 69 704 2013
PubMed-ID: 23722859  |  Reference-DOI: 10.1107/S1744309113011470
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOXIN ADTX1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPENTRE PLASMID
    Expression System StrainBL21
    Expression System Taxid562
    FragmentRHO-DA1A
    MutationYES
    OrganVENOM GLAND
    Organism CommonEASTERN GREEN MAMBA
    Organism ScientificDENDROASPIS ANGUSTICEPS
    Organism Taxid8618
    StrainANGUSTICEPS
    SynonymRHO-EPTX-DA1A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:0 , ASP A:16 , ASN A:51 , HOH A:231 , HOH A:261BINDING SITE FOR RESIDUE EDO A 101
2AC2SOFTWAREPRO A:18 , ASP A:19 , GLN A:21 , VAL A:32 , PRO A:33 , ILE A:35BINDING SITE FOR RESIDUE PEG A 102
3AC3SOFTWAREGLY A:11 , LEU A:23 , CYS A:46 , CYS A:57 , LYS A:59 , HOH A:239BINDING SITE FOR RESIDUE PEG A 103

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:24
2A:17 -A:42
3A:46 -A:57
4A:58 -A:63

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IYE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IYE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IYE)

(-) Exons   (0, 0)

(no "Exon" information available for 4IYE)

(-) 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:66
                                                                                                 
               SCOP domains d4iyea_ A: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..eeeeee......eeeeeeeeee..eeeeeeeee..........eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  4iye A  0 GLTCVTSKSIFGITTEDCPDGQNLCFKRRHYVVPAIYDSTRGCAATCPIPENYDSIHCCKTDKCNE 65
                                     9        19        29        39        49        59      

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IYE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IYE)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4iye)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4iye
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  3SI1A_DENAN | P85092
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  3SI1A_DENAN | P85092
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4IYE)

(-) Related Entries Specified in the PDB File

1ff4 X-RAY STRUCTURE OF MUSCARINIC TOXIN 2 AT 1.5 ANGSTROM RESOLUTION
2h5f DENMOTOXIN: A THE THREE-FINGER TOXIN FROM COLUBRID SNAKE BOIGA DENDROPHILA WITH BIRD-SPECIFIC ACTIVITY
2h7z CRYSTAL STRUCTURE OF IRDITOXIN
2vlw CRYSTAL STRUCTURE OF THE MUSCARINIC TOXIN MT7 DIIODOTYR51 DERIVATIVE
3fev CRYSTAL STRUCTURE OF THE CHIMERIC MUSCARINIC TOXIN MT7 WITH LOOP 1 FROM MT1
3neq CRYSTAL STRUCTURE OF THE CHIMERIC MUSCARINIC TOXIN MT7 WITH LOOP 3 FROM MT1
4do8 CRYSTAL STRUCTURE OF THE MUSCARINIC TOXIN MT1