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 :  FOLDON DOMAIN WILD TYPE N-CONJUGATE
 
Authors :  M. A. Graewert, A. Berthelmann, J. Lach, M. Groll, J. Eichler
Date :  25 Oct 13  (Deposition) - 12 Mar 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Trimeric Scaffold, Chemical Ligation, Folding, Trazido-Functionalized Trimesic Acid Scaffold, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Berthelmann, J. Lach, M. A. Grawert, M. Groll, J. Eichler
Versatile C(3)-Symmetric Scaffolds And Their Use For Covalent Stabilization Of The Foldon Trimer.
Org. Biomol. Chem. V. 12 2606 2014
PubMed-ID: 24637609  |  Reference-DOI: 10.1039/C3OB42251H

(-) Compounds

Molecule 1 - FIBRITIN
    Chains: A, B, C
    Engineered: YES
    Fragment: C-TERMINUS FRAGMENT (UNP RESIDUES 458-484)
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN BACTERIOPHAGE T4 FIBRITIN AT ITS C-TERMINUS AND HARBORS AN TRIMESIC ACID N-CONJUGATE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 4NCV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NCV)

(-) 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:28
                                                           
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ............eeeee..eeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  4ncv A  0 xGYIPEAPRDGQAYVRKDGEWVLLSTFL 27
                            |        9        19        
                            |                           
                            0-ACE                       


Chain B from PDB  Type:PROTEIN  Length:28
                                                           
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .............eeee..eeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  4ncv B  0 xGYIPEAPRDGQAYVRKDGEWVLLSTFL 27
                            |        9        19        
                            0-ACE                       


Chain C from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ............eeee..eeee.hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  4ncv C  1 GYIPEAPRDGQAYVRKDGEWVLLSTFL 27
                                    10        20
   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 4NCV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4ncv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ncv)
 

(-) 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
  4ncv
    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
  D9IEJ2_BPT4 | D9IEJ2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  WAC_BPT4 | P10104
    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
  D9IEJ2_BPT4 | D9IEJ2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  WAC_BPT4 | P10104
    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
        D9IEJ2_BPT4 | D9IEJ2: 4ncu 4ncw
        WAC_BPT4 | P10104: 1aa0 1avy 1ox3 1rfo 1v1h 1v1i 2bsg 2ibl 2kbl 3a1m 3j2o 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4ncu 4ncw
UniProtKB/TrEMBL
        D9IEJ2_BPT4 | D9IEJ2: 4zyp 5c0r 5c0s

(-) Related Entries Specified in the PDB File

1fro TRIMERIC FOLDON OF THE T4 PHAGEHEAD FIBRITIN (NMR STRUCTURE)
4ncu FOLDON DOMAIN WILD TYPE (X-RAY)
4ncw