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 :  SEQUENCE IENKAD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE A6
 
Authors :  M. D. Hartmann, C. T. Mendler, A. N. Lupas, B. Hernandez Alvarez
Date :  17 Sep 15  (Deposition) - 27 Jan 16  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Protein, Alpha/Beta Coiled Coil, Beta Layer, Trimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Hartmann, C. T. Mendler, J. Bassler, I. Karamichali, O. Ridderbusch, A. N. Lupas, B. Hernandez Alvarez
Alpha / Beta Coiled Coils.
Elife V. 5 2016
PubMed-ID: 26771248  |  Reference-DOI: 10.7554/ELIFE.11861

(-) Compounds

Molecule 1 - GENERAL CONTROL PROTEIN GCN4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5APQ)

(-) Sites  (0, 0)

(no "Site" information available for 5APQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5APQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5APQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5APQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5APQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5APQ)

(-) 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:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5apq A  3 QLEDKVEELLSKVYHLENEVARLKKLIENKADMKQLEDKVEELLSKVYHLENEVARLKKLV 63
                                    12        22        32        42        52        62 


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5apq B  3 QLEDKVEELLSKVYHLENEVARLKKLIENKADMKQLEDKVEELLSKVYHLENEVARLKKLV 63
                                    12        22        32        42        52        62 


Chain C from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5apq C  3 QLEDKVEELLSKVYHLENEVARLKKLIENKADMKQLEDKVEELLSKVYHLENEVARLKKLV 63
                                    12        22        32        42        52        62
   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 5APQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5APQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5APQ)

(-) Gene Ontology  (25, 25)

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 5apq)
 
  Sites
(no "Sites" information available for 5apq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5apq)
 

(-) 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
  5apq
    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
  GCN4_YEAST | P03069
    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
  GCN4_YEAST | P03069
    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
        GCN4_YEAST | P03069: 1ce9 1dgc 1env 1fav 1fmh 1gcl 1gcm 1gk6 1gzl 1ihq 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2ahp 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2efr 2efs 2g9j 2hy6 2ipz 2k8x 2lpb 2n9b 2nrn 2o7h 2ovn 2vky 2vnl 2wg5 2wg6 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2yny 2ynz 2yo0 2yo1 2yo2 2yo3 2z5h 2z5i 2zta 3azd 3bas 3bat 3ck4 3crp 3g9r 3gjp 3i1g 3i5c 3k7z 3m48 3p8m 3zmf 4c46 4dmd 4g2k 4hu5 4hu6 4niz 4nj0 4nj1 4nj2 4owi 4tl1 5app 5aps 5apt 5apu 5apv 5apw 5apx 5apy 5apz 5iew 5iir 5iiv 5kht

(-) Related Entries Specified in the PDB File

5app ACTINOBACILLUS ACTINOMYCETEMCOMITANS OMP100 RESIDUES 133-198 FUSED TO GCN4 ADAPTORS
5aps SEQUENCE IENKKAD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE A7
5apt SEQUENCE IENKADKAD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE A9
5apu SEQUENCE IANKEDKAD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE A9B BLACK
5apv SEQUENCE IANKEDKAD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE A9B GREY
5apw SEQUENCE MATKDD INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE T6
5apx SEQUENCE MATKDDIAN INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE T9(6)
5apy SEQUENCE MATKDDIAN INSERTED BETWEEN GCN4 ADAPTORS - STRUCTURE T9(9)
5apz THERMOSINUS CARBOXYDIVORANS NOR1 TCAR0761 RESIDUES 68-101 AND 191- 211 FUSED TO GCN4 ADAPTORS