Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE ATL1 IN COMPLEX WITH DAMAGED DNA CONTAINING O6-CARBOXYMETHYLGUANINE
 
Authors :  J. L. Tubbs, A. S. Arvai, J. A. Tainer
Date :  13 Apr 12  (Deposition) - 20 Jun 12  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Alkyltransferase, Dna Repair, Nucleotide Excision Repair, Ner, Base Repair, Dna, Dna Damage, Guanine, Alkylation, Dna Binding Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. F. Latypov, J. L. Tubbs, A. J. Watson, A. S. Marriott, G. Mcgown, M. Thorncroft, O. J. Wilkinson, P. Senthong, A. Butt, A. S. Arvai, C. L. Millington, A. C. Povey, D. M. Williams, M. F. Santibanez-Koref, J. A. Tainer, G. P. Margison
Atl1 Regulates Choice Between Global Genome And Transcription-Coupled Repair Of O(6)-Alkylguanines.
Mol. Cell V. 47 50 2012
PubMed-ID: 22658721  |  Reference-DOI: 10.1016/J.MOLCEL.2012.04.028

(-) Compounds

Molecule 1 - ALKYLTRANSFERASE-LIKE PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATL1, SPAC1250.04C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE 972H-
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
 
Molecule 2 - RNA (5'-R(*GP*CP*CP*AP*TP*GP*(C6G)P*CP*TP*AP*GP*TP*A)-3')
    Chains: C, D, E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1C6G4Mod. Nucleotide6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1C6G2Mod. Nucleotide6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1C6G2Mod. Nucleotide6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE

(-) Sites  (0, 0)

(no "Site" information available for 4ENN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ENN)

(-) Sequences/Alignments

Asymmetric 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:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.......eehhhhhhhh.hhhhhhhhhhhhhhh......hhh.ee..............hhhhhhhhhhh....eee..eeee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4enn A   1 MRMDEFYTKVYDAVCEIPYGKVSTYGEIARYVGMPSYARQVGQAMKHLHPETHVPWHRVINSRGTISKRDISAGEQRQKDRLEEEGVEIYQTSLGEYKLNLPEYMWKP 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....eehhhhhhhh.hhhhhhhhhhhhhhh......hhh.ee..............hhhhhhhhhhh....eee..eeee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4enn B   1 MRMDEFYTKVYDAVCEIPYGKVSTYGEIARYVGMPSYARQVGQAMKHLHPETHVPWHRVINSRGTISKRDISAGEQRQKDRLEEEGVEIYQTSLGEYKLNLPEYMWKP 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain C from PDB  Type:DNA  Length:13
                                             
                 4enn C   1 GCCATGgCTAGTA  13
                                  | 10   
                                  7-C6G  


Chain D from PDB  Type:DNA  Length:13
                                             
                 4enn D   1 GCCATGgCTAGTA  13
                                  | 10   
                                  7-C6G  


Chain E from PDB  Type:DNA  Length:13
                                             
                 4enn E   1 GCCATGgCTAGTA  13
                                  | 10   
                                  7-C6G  


Chain F from PDB  Type:DNA  Length:13
                                             
                 4enn F   1 GCCATGgCTAGTA  13
                                  | 10   
                                  7-C6G
   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 4ENN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    C6G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4enn)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4enn)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4enn
    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
  ATL1_SCHPO | Q9UTN9
    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
  ATL1_SCHPO | Q9UTN9
    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
        ATL1_SCHPO | Q9UTN9: 3gva 3gx4 3gyh 4enj 4enk 4enm 4hdu 4hdv

(-) Related Entries Specified in the PDB File

4enj 4enk 4enm