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 :  HUAB-19BP
 
Authors :  M. Hammel, F. E. Reyes, R. Parpana, J. A. Tainer, S. Adhya, D. Amlanjyoti
Date :  24 Feb 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hu-Dna, Transcription, Pathogenicity, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hammel, F. E. Reyes, R. Parpana, J. A. Tainer, S. Adhya, D. Amlanjyot
Structure Of Huab-19Bp Dna Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN HU-BETA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HUPB, HOPD, B0440, JW0430
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - SYNTHETIC DNA STRAND
    Chains: B
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 3 - SYNTHETIC DNA STRAND
    Chains: D
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 4 - DNA-BINDING PROTEIN HU-ALPHA
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HUPA, B4000, JW3964
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: HU-2,NS2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4YEW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YEW)

(-) 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:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeee...eeeeeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4yew A  1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKEAKVPSFRAGKALKDAVN 90
                                    10        20        30        40        50   ||   79        89 
                                                                                54|                
                                                                                 74                


Chain B from PDB  Type:DNA  Length:9
                                        
                  4yew B -4 CCCCCACAC  4


Chain C from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeee...eeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  4yew C  1 MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRNVPAFVSGKALKDAVK 90
                                    10        20        30        40        50    ||  79        89 
                                                                                 55|               
                                                                                  75               


Chain D from PDB  Type:DNA  Length:11
                                          
                  4yew D 10 CACACACAGAC 20
                                    19
   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 4YEW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 22)

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 4yew)
 
  Sites
(no "Sites" information available for 4yew)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4yew)
 

(-) 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
  4yew
    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
  DBHA_ECO57 | P0ACF2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DBHA_ECOLI | P0ACF0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DBHB_ECOLI | P0ACF4
    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
  DBHA_ECO57 | P0ACF2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DBHA_ECOLI | P0ACF0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DBHB_ECOLI | P0ACF4
    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
        DBHA_ECO57 | P0ACF2: 4yex 4yey 4yf0 4yfh 4yft
        DBHA_ECOLI | P0ACF0: 1mul 2o97 4yex 4yey 4yf0 4yfh 4yft
        DBHB_ECOLI | P0ACF4: 2o97 4p3v 4yft

(-) Related Entries Specified in the PDB File

4yex 4yey 4yf0 4yfh 4yft