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 :  STRUCTURE OF PORCINE CYCLIC GMP AMP SYNTHASE (CGAS) IN COMPLEX WITH DNA, ATP AND GTP
 
Authors :  T. Deimling, K. -P. Hopfner
Date :  23 Apr 13  (Deposition) - 05 Jun 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.08
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oas-Like Fold, Receptor, Immunity, Cgas, Double Stranded Dna, Gtp, Cytosol, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Civril, T. Deimling, C. C. De Oliveira Mann, A. Ablasser, M. Moldt G. Witte, V. Hornung, K. P. Hopfner
Structural Mechanism Of Cytosolic Dna Sensing By Cgas.
Nature V. 498 332 2013
PubMed-ID: 23722159  |  Reference-DOI: 10.1038/NATURE12305

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 135-495
    Gene: MB21D1
    Organism Common: PIGS,SWINE,WILD BOAR
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
 
Molecule 2 - DNA (5'-D(P*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
    Chains: B, C
    Engineered: YES
    Organism Scientific: SYNTHETIC DNA
    Organism Taxid: 32630
    Other Details: 14MER DS DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:367 , CYS A:373 , CYS A:374 , CYS A:381BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARETHR A:186 , MET A:204 , GLY A:279 , SER A:280 , PRO A:281 , ASP A:296 , ILE A:298 , ARG A:353 , SER A:355 , SER A:357 , ATP A:503BINDING SITE FOR RESIDUE GTP A 502
3AC3SOFTWAREGLY A:187 , SER A:188 , GLU A:191 , GLN A:200 , ASN A:202 , ARG A:353 , SER A:357 , GLU A:360 , LYS A:391 , SER A:412 , TYR A:413 , LYS A:416 , GTP A:502 , MG A:504BINDING SITE FOR RESIDUE ATP A 503
4AC4SOFTWARESER A:188 , GLN A:200 , ASN A:202 , ATP A:503BINDING SITE FOR RESIDUE MG A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KB6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:137 -Lys A:138
2Lys A:289 -Pro A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KB6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KB6)

(-) Exons   (0, 0)

(no "Exon" information available for 4KB6)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeeehhhhhh.......eeeeeeeee....eeee......eeeee......ee..eehhhhhhhhhhhhhhhhhhhhh...eee........eeeeee.....eeeeeeeeeee....hhhhh....hhhhhhhhhhhhhhhh.eeee...........eeeehhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kb6 A 135 GAWKLQTVLEKVRLSRHEISEAAEVVNWVVEHLLRRLQGGESEFKGVALLRTGSYYERVKISAPNQFNVMFKLEVPRIQLEEYCNSGAHYFVKFPLEQFLEKEILSASKMLSKFRKIIKEEIKNIEDTGVTVERKRRGSPAVTLLISKPKEISVDIILALESKSSWPASTQKGLPISQWLGAKVKNNLKRQPFYLVPKHAKGFQEETWRLSFSHIEKDILKNHGQSKTCCEIDGVKCCRKECLKLMKYLLEQLKKKFGNRRELAKFCSYHVKTAFFHVCTQDPHDNQWHLKNLECCFDNCVAYFLQCLKTEQLANYFIPGVNLFSRDLIDKPSKEFLSKQIEYERNNGFPVFW 497
                                   144       154       164       174       184       194       204       214       224   ||  241       251       261       271       281       291       301       311       321       331       341||     354       364       374       384       394       404       414       424       434       444       454       464       474       484       494   
                                                                                                                       228|                                                                                                       342|                                                                                                                                                       
                                                                                                                        236                                                                                                        346                                                                                                                                                       


Chain B from PDB  Type:DNA  Length:14
                                              
                 4kb6 B   1 CGACGCTAGCGTCG  14
                                    10    


Chain C from PDB  Type:DNA  Length:13
                                             
                 4kb6 C   2 GACGCTAGCGTCG  14
                                    11
   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 4KB6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KB6)

(-) Gene Ontology  (17, 17)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:289 - Pro A:290   [ RasMol ]  
    Trp A:137 - Lys A:138   [ RasMol ]  
 

(-) 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
  4kb6
    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
  CGAS_PIG | I3LM39
    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
  CGAS_PIG | I3LM39
    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
        CGAS_PIG | I3LM39: 4jlx 4jlz

(-) Related Entries Specified in the PDB File

4jlx 4jlz