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 :  CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-6) POSITION
 
Authors :  W. Wang, L. S. Beese
Date :  04 Aug 11  (Deposition) - 19 Oct 11  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase I, Protein-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, H. W. Hellinga, L. S. Beese
Structural Evidence For The Rare Tautomer Hypothesis Of Spontaneous Mutagenesis.
Proc. Natl. Acad. Sci. Usa V. 108 17644 2011
PubMed-ID: 22006298  |  Reference-DOI: 10.1073/PNAS.1114496108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE I
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BACILLUS FRAGMENT (UNP RESIDUES 285-876)
    Organism Scientific: GEOBACILLUS
    Organism Taxid: 129337
 
Molecule 2 - 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*CP*GP*TP*C)-3'
    Chains: B
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
    Chains: C
    Engineered: YES
    Other Details: TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION
3SUC2Ligand/IonSUCROSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:45 , HOH A:117 , HOH A:139 , GLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , LEU A:395 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:999 , HOH A:1005 , HOH A:1073BINDING SITE FOR RESIDUE SUC A 901
2AC2SOFTWAREHOH A:113 , HOH A:146 , HOH A:148 , GLU A:540 , GLN A:543 , TYR A:554 , GLN A:755 , LYS A:758 , ARG A:784 , GLU A:788 , HOH A:913BINDING SITE FOR RESIDUE SUC A 902
3AC3SOFTWARELYS A:298 , MET A:299 , ALA A:300 , ARG A:343 , ARG A:677 , HOH A:1167BINDING SITE FOR RESIDUE SO4 A 1
4AC4SOFTWAREHIS A:682 , ARG A:702 , LYS A:706BINDING SITE FOR RESIDUE SO4 A 2
5AC5SOFTWAREHOH A:174 , ARG A:779 , ARG A:819BINDING SITE FOR RESIDUE SO4 A 3
6AC6SOFTWAREHOH A:54 , ASP A:653 , TYR A:654 , ASP A:830BINDING SITE FOR RESIDUE MG A 877

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TAR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:620 -Pro A:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TAR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TAR)

(-) Exons   (0, 0)

(no "Exon" information available for 3TAR)

(-) 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:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d3tara1 A:297-468 automated matches                                                                                                                                         d3tara2 A:469-876 automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tar A 297 AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876


Chain B from PDB  Type:DNA  Length:15
                                               
                 3tar B  20 GCGATCACGCACGTC  34
                                    29     


Chain C from PDB  Type:DNA  Length:16
                                                
                 3tar C   4 GACGTACGTGATCGCA  19
                                    13
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TAR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TAR)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3TAR)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:620 - Pro A:621   [ 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
  3tar
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.7
    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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3TAR)

(-) Related Entries Specified in the PDB File

3tan CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-1) POSITION
3tap CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-3) POSITION
3taq CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-4) POSITION
3thv CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDATP-DT IN CLOSED CONFORMATION
3ti0 CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDGTP-DC IN CLOSED CONFORMATION