Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - 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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURES OF THE CALCIUM-BOUND CON-G AND CON-T(K7GLU) DIMERIC PEPTIDES DEMONSTRATE A NOVEL METAL-DEPENDENT HELIX-FORMING MOTIF
 
Authors :  S. E. Cnudde, M. Prorok, Q. Dai, F. J. Castellino, J. H. Geiger
Date :  13 May 06  (Deposition) - 24 Apr 07  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Conantoxin, Con-T, Nmdar Antagonist, Gla-Containing, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Cnudde, M. Prorok, Q. Dai, F. J. Castellino, J. H. Geiger
The Crystal Structures Of The Calcium-Bound Con-G And Con-T[K7Gamma] Dimeric Peptides Demonstrate A Metal-Dependent Helix-Forming Motif
J. Am. Chem. Soc. V. 129 1586 2007
PubMed-ID: 17243678  |  Reference-DOI: 10.1021/JA065722Q

(-) Compounds

Molecule 1 - CONANTOKIN-T
    Chains: A, B
    Engineered: YES
    Mutation: YES
    Organism Common: FISH-HUNTING CONE SNAIL
    Organism Scientific: CONUS TULIPA
    Organism Taxid: 6495
    Other Details: CON-T(K7GLU) WAS SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN CONUS TULIPA (TULIP CONE)
    Synonym: CON-T
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CGU10Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU10Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU5Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 3 (1, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU20Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECGU A:10 , CGU A:14 , HOH A:115 , CGU B:7 , CGU B:10 , HOH B:146BINDING SITE FOR RESIDUE CA B 101
2AC2SOFTWARECGU A:3 , CGU A:7 , HOH A:130 , CGU B:14BINDING SITE FOR RESIDUE CA A 102
3AC3SOFTWARECGU A:7 , CGU A:10 , HOH A:136 , CGU B:10 , CGU B:14 , HOH B:137BINDING SITE FOR RESIDUE CA B 103
4AC4SOFTWARECGU A:14 , CGU B:3 , CGU B:7 , HOH B:133BINDING SITE FOR RESIDUE CA B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DPR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DPR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DPR)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONANTOKINPS60025 Conantokin family signature.CKT_CONTU1-14
 		  2A:1-14
B:1-14
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONANTOKINPS60025 Conantokin family signature.CKT_CONTU1-14
 		  2A:1-14
B:1-14
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONANTOKINPS60025 Conantokin family signature.CKT_CONTU1-14
 		  2A:1-14
B:1-14
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CONANTOKINPS60025 Conantokin family signature.CKT_CONTU1-14
 		  4A:1-14
B:1-14

(-) Exons   (0, 0)

(no "Exon" information available for 2DPR)

(-) 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:21
 aligned with CKT_CONTU | P17684 from UniProtKB/Swiss-Prot  Length:21

    Alignment length:21
                                    10        20 
             CKT_CONTU    1 GEEEYQKMLENLREAEVKKNA 21
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE CONANTOKIN    ------- PROSITE
                 Transcript --------------------- Transcript
                  2dpr A  1 GEeeYQeMLeNLReAEVKKNA 21
                              ||  | 10   |    20 
                              ||  |  |   |       
                              3-CGU  |   |       
                               4-CGU |   |       
                                  7-CGU  |       
                                    10-CGU       
                                        14-CGU   


Chain B from PDB  Type:PROTEIN  Length:21
 aligned with CKT_CONTU | P17684 from UniProtKB/Swiss-Prot  Length:21

    Alignment length:21
                                    10        20 
             CKT_CONTU    1 GEEEYQKMLENLREAEVKKNA 21
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE CONANTOKIN    ------- PROSITE
                 Transcript --------------------- Transcript
                  2dpr B  1 GEeeYQeMLeNLReAEVKKNA 21
                              ||  | 10   |    20 
                              3-CGU  |   |       
                               4-CGU |   |       
                                  7-CGU  |       
                                    10-CGU       
                                        14-CGU
   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  (0, 0)

(no "SCOP Domain" information available for 2DPR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DPR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DPR)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CKT_CONTU | P17684)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CGU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dpr)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2dpr
    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
  CKT_CONTU | P17684
    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
  CKT_CONTU | P17684
    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
        CKT_CONTU | P17684: 1ont

(-) Related Entries Specified in the PDB File

2dpq A DIFFERENT PEPTIDE, CON-G BOUND TO CALCIUM.