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 SULFOLOBUS SOLFATARICUS O6-METHYLGUANINE METHYLTRANSFERASE IN COMPLEX WITH MODIFIED DNA
 
Authors :  R. Miggiano, F. Rossi, M. Rizzi
Date :  21 May 15  (Deposition) - 12 Aug 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A (1x),B (1x),C (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x)
Keywords :  Transferase, Extremophiles, Dna Repair, Alkylated Dna-Protein Alkyltransferase, Protein-Dna Complex, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Perugino, R. Miggiano, M. Serpe, A. Vettone, A. Valenti, S. Lahiri, F. Rossi, M. Rossi, M. Rizzi, M. Ciaramella
Structure-Function Relationships Governing Activity And Stability Of A Dna Alkylation Damage Repair Thermostable Protein.
Nucleic Acids Res. V. 43 8801 2015
PubMed-ID: 26227971  |  Reference-DOI: 10.1093/NAR/GKV774

(-) Compounds

Molecule 1 - METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE31
    Expression System Taxid: 469008
    Gene: OGT, SSO2487
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Other Details: METHIONINE AT POSITION 1 AND GLUTAMIC ACID AT POSITION 151 WERE NOT DETECTED IN ELECTRON DENSITY MAP. THEREFORE, THEY WERE EXCLUDED FROM THE COORDINATE FILE.
    Synonym: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE,MGMT,O-6- METHYLGUANINE-DNA-ALKYLTRANSFERASE
 
Molecule 2 - DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A (1x)B (1x)C (1x)
Biological Unit 2 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
16OG1Mod. Nucleotide6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
16OG-1Mod. Nucleotide6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16OG1Mod. Nucleotide6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4ZYD)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:29 -A:31

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZYD)

(-) 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.......eee..........hhhhhhhhhhhhhhhh...............hhhhhhhhhhhh.......eehhhhhhhhh.hhhhhhhhhhh.......hhh.ee..........hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zyd A   2 LVYGLYKSPLGYITVAKDDKGFIMLDFCDCVEGNSRDDSSFTEFFHKLDLYFEGKPINLREPINLKTYPFRLSVFKEVMKIPWGKVMTYKQIADSLGTSPRAVGMALSKNPILLIIPAHRVIAENGIGGYSRGVKLKRALLELEGVKIP 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         


Chain B from PDB  Type:DNA  Length:13
                                             
                 4zyd B   1 GCCATGxCTAGTA  13
                                  | 10   
                                  7-6OG  


Chain C from PDB  Type:DNA  Length:13
                                             
                 4zyd C  14 TACTAGCCATGGC  26
                                    23
   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 4ZYD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    6OG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4zyd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4zyd)
 
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
  4zyd
    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
  OGT_SULSO | Q97VW7
    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)
  2.1.1.63
    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
  OGT_SULSO | Q97VW7
    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
        OGT_SULSO | Q97VW7: 4zye 4zyg 4zyh 5llq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZYD)