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

(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDATP-DT IN CLOSED CONFORMATION
 
Authors :  W. Wang, L. S. Beese
Date :  19 Aug 11  (Deposition) - 19 Oct 11  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
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, D
    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)
    Mutation: YES
    Organism Scientific: GEOBACILLUS
    Organism Taxid: 129337
 
Molecule 2 - 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3'
    Chains: B, E
    Engineered: YES
    Other Details: PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3'
    Chains: C, F
    Engineered: YES
    Other Details: TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
12DA2Mod. Nucleotide2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2DDS2Ligand/Ion2',3'-DIDEOXYADENOSINE TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
12DA1Mod. Nucleotide2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2DDS1Ligand/Ion2',3'-DIDEOXYADENOSINE TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
12DA1Mod. Nucleotide2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2DDS1Ligand/Ion2',3'-DIDEOXYADENOSINE TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMG A:1 , ARG A:615 , ASP A:653 , TYR A:654 , SER A:655 , GLN A:656 , ILE A:657 , GLU A:658 , HIS A:682 , ARG A:702 , LYS A:706 , ALA A:707 , TYR A:710 , ASP A:830 , HOH A:881 , HOH A:899 , HOH A:1014 , HOH A:1040 , HOH A:1194 , HOH A:1280 , 2DA B:29 , DT C:3 , DT C:4BINDING SITE FOR RESIDUE DDS A 201
2AC2SOFTWAREDDS A:201 , ASP A:653 , TYR A:654 , ASP A:830BINDING SITE FOR RESIDUE MG A 1
3AC3SOFTWAREARG A:517 , ASN A:573 , HOH A:1392 , HOH A:1583 , LYS D:730BINDING SITE FOR RESIDUE SO4 A 2
4AC4SOFTWAREMG D:2 , HOH D:148 , HOH D:262 , ARG D:615 , TYR D:654 , SER D:655 , GLN D:656 , ILE D:657 , GLU D:658 , HIS D:682 , ARG D:702 , LYS D:706 , TYR D:710 , ASP D:830 , HOH D:948 , HOH D:972 , HOH D:1055 , HOH D:1149 , HOH D:1695 , HOH D:1696 , 2DA E:29 , DT F:3 , DT F:4BINDING SITE FOR RESIDUE DDS D 202
5AC5SOFTWAREDDS D:202 , TYR D:654 , ASP D:830 , HOH D:1696BINDING SITE FOR RESIDUE MG D 2
6AC6SOFTWAREMET D:299 , ALA D:300 , ARG D:343 , ARG D:677BINDING SITE FOR RESIDUE SO4 D 1
7AC7SOFTWAREHOH D:151 , THR D:857BINDING SITE FOR RESIDUE SO4 D 3

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:620 -Pro A:621
2Glu D:620 -Pro D:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3THV)

(-) 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:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3thv A 298 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         


Chain B from PDB  Type:DNA  Length:9
                                         
                 3thv B  21 CCTGACTCx  29
                                    |
                                   29-2DA


Chain C from PDB  Type:DNA  Length:12
                                            
                 3thv C   1 ATTTGAGTCAGG  12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhh..eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3thv D 298 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         


Chain E from PDB  Type:DNA  Length:9
                                         
                 3thv E  21 CCTGACTCx  29
                                    |
                                   29-2DA


Chain F from PDB  Type:DNA  Length:12
                                            
                 3thv F   1 ATTTGAGTCAGG  12
                                    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 3THV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    2DA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DDS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:620 - Pro A:621   [ RasMol ]  
    Glu D:620 - Pro D:621   [ RasMol ]  
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3thv
    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 3THV)

(-) 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
3tar CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DUPLEX DNA WITH CYTOSINE-ADENINE MISMATCH AT (N-6) POSITION
3ti0 CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDGTP-DC IN CLOSED CONFORMATION