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

(-) Description

Title :  CRYSTAL STRUCTURE OF CANAVALIA MARITIMA LECTIN (CONM) COMPLEXED WITH INTERLEUKIN - 1 BETA PRIMER
 
Authors :  D. B. H. A. Vieira, P. Delatorre, B. A. M. Rocha, C. S. Teixeira, J. C. Silv E. M. Lima, R. B. Nobrega, B. S. Cavada
Date :  10 Jul 14  (Deposition) - 22 Jul 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,D,G,H
Keywords :  Carbohydrate Binding Protein, Carbohydrate Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. B. H. A. Vieira, P. Delatorre, B. S. Cavada, R. B. Nobrega, C. S. Teixeira, J. C. Silva-Filho, E. M. Lima, B. A. M. Rocha
Crystal Structure Of Canavalia Maritima Lectin (Conm) Complexed With Interleukin 1 - Beta Primer
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CONCANAVALIN-A
    Chains: A, D
    Organism Common: BEACH BEAN
    Organism Scientific: CANAVALIA LINEATA
    Organism Taxid: 28957
    Synonym: CON A
 
Molecule 2 - DNA (5'-D(P*CP*G)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: INTERLEUKIN 1 - BETA PRIMER
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*C)-3')
    Chains: H
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: INTERLEUKIN 1 - BETA PRIMER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4TZD)

(-) Sites  (0, 0)

(no "Site" information available for 4TZD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TZD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:149 -Thr A:150
2Ala A:207 -Asp A:208
3Gly D:149 -Thr D:150
4Ala D:207 -Asp D:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TZD)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee.......eee.........eeeeeee....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee........eeeeeeeeeeee..eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeee...........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tzd A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKETNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110     ||125       135       145       155       165       175       185       195       205       215       225       235  
                                                                                                                                             116|                                                                                                                   
                                                                                                                                              122                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.............eeeeee......eeee.......eeeeeeee.....eeeeeee.....eeeeeee.hhhhhh..eeeeeeeee........eeeeeeeeeee...eeeeeee.........eeeee..ee.....ee..............eeeeee...ee........eeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tzd D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKETNALHFVFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSSDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110     ||125       135       145       155       165       175       185       195       205       215       225       235  
                                                                                                                                             116|                                                                                                                   
                                                                                                                                              122                                                                                                                   


Chain G from PDB  Type:DNA  Length:2
                                  
                 4tzd G   1 CG   2


Chain H from PDB  Type:DNA  Length:2
                                  
                 4tzd H   1 TC   2
   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 4TZD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
(no "Ligands, Modified Residues, Ions" information available for 4tzd)
 
  Sites
(no "Sites" information available for 4tzd)
 
  Cis Peptide Bonds
    Ala A:207 - Asp A:208   [ RasMol ]  
    Ala D:207 - Asp D:208   [ RasMol ]  
    Gly A:149 - Thr A:150   [ RasMol ]  
    Gly D:149 - Thr D:150   [ RasMol ]  
 

(-) 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 ](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
  4tzd
    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
  CONA_CANLI | P81460
    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
  CONA_CANLI | P81460
    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
        CONA_CANLI | P81460: 2cwm 2cy6 2cyf 3snm 4dpn 4i30 4tys 5byn

(-) Related Entries Specified in the PDB File

4tys