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

(-) Description

Title :  COMPLEX OF ESCHERICHIA COLI DNA ADENINE METHYLTRANSFERASE (DAM) WITH ADOHCY AND WITH DNA CONTAINING PROXIMAL PAP REGULON SEQUENCE
 
Authors :  J. R. Horton, X. Cheng
Date :  15 Nov 14  (Deposition) - 15 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,F,G
Keywords :  Dam Methylation, Gatc Recognition, Base Flipping, Bacterial Virulence, Methylation-Independent Transcriptional Repressor, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, X. Zhang, R. M. Blumenthal, X. Cheng
Structures Of Escherichia Coli Dna Adenine Methyltransferas (Dam) In Complex With A Non-Gatc Sequence: Potential Implications For Methylation-Independent Transcriptional Repression.
Nucleic Acids Res. V. 43 4296 2015
PubMed-ID: 25845600  |  Reference-DOI: 10.1093/NAR/GKV251

(-) Compounds

Molecule 1 - DNA ADENINE METHYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DAM, ECMDS42_2833
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 1110693
    Strain: K-12 SUBSTR. MDS42
 
Molecule 2 - DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:10 , ALA A:11 , GLY A:12 , PRO A:34 , PHE A:35 , VAL A:36 , GLY A:37 , ALA A:38 , SER A:40 , ASP A:54 , ILE A:55 , SER A:164 , TYR A:165 , ASP A:181 , PRO A:182 , PRO A:183 , TYR A:184 , PHE A:201 , HOH A:429BINDING SITE FOR RESIDUE SAH A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RTN)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee..........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh.....eee.........eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rtn A   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDSSVVYCDPPYAPLSSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVRRSKKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     ||203       213       223       233       243      |261         
                                                                                                                                                                                                                   188|                                               250|           
                                                                                                                                                                                                                    200                                                259           


Chain F from PDB  Type:DNA  Length:11
                                           
                 4rtn F   1 TTTAAAGATCG  11
                                    10 


Chain G from PDB  Type:DNA  Length:11
                                           
                 4rtn G   1 ACGATCTTTAA  11
                                    10
   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 4RTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rtn)
 

(-) 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 | Asym./Biol. Unit - sites 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
  4rtn
    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
  DMA_ECOLI | P0AEE8
    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
  DMA_ECOLI | P0AEE8
    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
        DMA_ECOLI | P0AEE8: 2g1p 2ore 4gbe 4gol 4gom 4gon 4goo 4rtj 4rtk 4rtl 4rtm 4rto 4rtp 4rtq 4rtr 4rts

(-) Related Entries Specified in the PDB File

2g1p STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE (DAM) WITH COGNATE SEQUENCE
2ore BINARY STRUCTURE OF E.COLI DAM
4rtj
4rtk
4rtl
4rtm
4rto
4rtp
4rtq
4rtr
4rts