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

(-) Description

Title :  HIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR AND MINOR GROOVE INTERACTIONS
 
Authors :  J. -A. Feng, R. C. Johnson, R. E. Dickerson
Date :  17 Dec 93  (Deposition) - 30 Apr 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Feng, R. C. Johnson, R. E. Dickerson
Hin Recombinase Bound To Dna: The Origin Of Specificity In Major And Minor Groove Interactions.
Science V. 263 348 1994
PubMed-ID: 8278807
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3')
    Chains: B
    Engineered: YES
 
Molecule 2 - DNA (5'- D(*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3')
    Chains: C
    Engineered: YES
 
Molecule 3 - PROTEIN (HIN RECOMBINASE)
    Chains: A
    Engineered: YES

 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 1HCR)

(-) Sites  (0, 0)

(no "Site" information available for 1HCR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HCR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HCR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HCR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HCR)

(-) Exons   (0, 0)

(no "Exon" information available for 1HCR)

(-) 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:52
 aligned with HIN_SALTY | P03013 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:52
                                   148       158       168       178       188  
            HIN_SALTY   139 GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASRIKKRMN 190
               SCOP domains d1hcra_ A: HIN recombinase (DNA-binding domain)      SCOP domains
               CATH domains 1hcrA00 A:139-190 Homeodomain-like                   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 1hcr A 139 GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN 190
                                   148       158       168       178       188  


Chain B from PDB  Type:DNA  Length:14
                                              
                 1hcr B   2 TGTTTTTGATAAGA  15
                                    11    


Chain C from PDB  Type:DNA  Length:13
                                             
                 1hcr C  17 TCTTATCAAAAAC  29
                                    26
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HCR)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HIN_SALTY | P03013)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000150    recombinase activity    Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

 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 1hcr)
 
  Sites
(no "Sites" information available for 1hcr)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hcr)
 

(-) 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)
Midas
  DNA: ribbon, plates; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  DNA: ribbon, plates; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  sticks
[ mono GIF format | stereo GIF format ]
  spacefill
[ mono GIF format | stereo GIF format ]
Setor
  DNA: ribbon, sticks; protein: ribbon; water
[ mono GIF format | stereo GIF format ]
  spacefill, water
[ mono GIF format | stereo GIF format ]
  ribbon, sticks
[ mono GIF format | stereo GIF format ]
  spacefill
[ mono GIF format | stereo GIF format ]
Weblab
  DNA: ribbon; protein: ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  DNA: ribbon, lines, labeling; protein: surface, molecular electrostatic potential coloring
[ mono GIF format | stereo GIF format ]
  DNA: ribbon, lines; protein: ribbon, secondary structure; labeling, water
[ mono GIF format | stereo GIF format ]
  DNA: ribbon, lines; protein: spacefill; labeling , water
[ mono GIF format | stereo GIF format ]
  DNA: spacefill; protein: ribbon, secondary structure, lines; labeling, water
[ mono GIF format | stereo GIF format ]
  surface, molecular electrostatic potential coloring
[ mono GIF format | stereo GIF format ]
  DNA: ribbon, lines; protein: ribbon, secondary structure, lines; water; labeling; detailed view
[ mono GIF format | stereo GIF format ]
  DNA: spacefill; protein: ribbon, lines; labeling ; water
[ mono GIF format | stereo GIF format ]
Distance Plot
  representative atoms: CA, O3*
[ mono GIF format | mono PDF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1hcr
    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
  HIN_SALTY | P03013
    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
  HIN_SALTY | P03013
    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
        HIN_SALTY | P03013: 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HCR)