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 :  POLYMERASE-DNA COMPLEX
 
Authors :  D. T. Nair, A. Sharma
Date :  14 Jan 13  (Deposition) - 10 Apr 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B,C,F,G,H
Biol. Unit 1:  F,G,H  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Dna Polymerase, Y-Family, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sharma, J. Kottur, N. Narayanan, D. T. Nair
A Strategically Located Serine Residue Is Critical For The Mutator Activity Of Dna Polymerase Iv From Escherichia Coli
Nucleic Acids Res. V. 41 5104 2013
PubMed-ID: 23525461  |  Reference-DOI: 10.1093/NAR/GKT146

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*CP*TP*GP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: G, B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - DNA POLYMERASE IV
    Chains: F, A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Gene: B0231, DINB, DINP, JW0221
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: POL IV

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCFGH
Biological Unit 1 (1x):    FGH
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
10KX2Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10KX1Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10KX1Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP F:8 , MET F:9 , ASP F:10 , CYS F:11 , PHE F:12 , PHE F:13 , SER F:42 , THR F:43 , ARG F:49 , ASP F:103 , LYS F:157 , MG F:402 , MG F:403 , HOH F:502 , HOH F:514 , HOH F:518 , HOH F:536 , DG G:840 , DC H:873BINDING SITE FOR RESIDUE 0KX F 401
2AC2SOFTWAREASP F:8 , MET F:9 , ASP F:103 , 0KX F:401 , MG F:403 , HOH F:502BINDING SITE FOR RESIDUE MG F 402
3AC3SOFTWAREASP F:8 , ASP F:103 , GLU F:104 , 0KX F:401 , MG F:402 , HOH F:502 , HOH F:518BINDING SITE FOR RESIDUE MG F 403
4AC4SOFTWAREASP A:8 , MET A:9 , ASP A:10 , CYS A:11 , PHE A:12 , PHE A:13 , SER A:42 , THR A:43 , ARG A:49 , ASP A:103 , LYS A:157 , MG A:402 , MG A:403 , HOH A:516 , HOH A:517 , DG B:840 , DC C:873BINDING SITE FOR RESIDUE 0KX A 401
5AC5SOFTWAREASP A:8 , MET A:9 , ASP A:103 , 0KX A:401 , MG A:403BINDING SITE FOR RESIDUE MG A 402
6AC6SOFTWAREASP A:8 , ASP A:103 , GLU A:104 , 0KX A:401 , MG A:402BINDING SITE FOR RESIDUE MG A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys F:157 -Pro F:158
2Lys A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IRC)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhh..eee....eeeee..........hhhhhhhhhh.........eeeeee.hhhhhhhhhhhh....eee....hhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irc A   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALALCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQACDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain B from PDB  Type:DNA  Length:18
                                                  
                 4irc B 837 TCTGGGGTCCTAGGACCC 854
                                   846        


Chain C from PDB  Type:DNA  Length:17
                                                 
                 4irc C 857 CTAGGGTCCTAGGACCC 873
                                   866       


Chain F from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee.hhhhh.eeeeehhhhhh......eehhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eee....eeeee.........hhhhhhhhhhhhhh......eeeeee.hhhhhhhhhh......eee....hhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irc F   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALALCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQACDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain G from PDB  Type:DNA  Length:18
                                                  
                 4irc G 837 TCTGGGGTCCTAGGACCC 854
                                   846        


Chain H from PDB  Type:DNA  Length:14
                                              
                 4irc H 860 GGGTCCTAGGACCC 873
                                   869
   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 4IRC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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
    0KX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
    Lys A:157 - Pro A:158   [ RasMol ]  
    Lys F:157 - Pro F:158   [ 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
  4irc
    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
  DPO4_ECOLI | Q47155
    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)
  2.7.7.7
    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
  DPO4_ECOLI | Q47155
    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
        DPO4_ECOLI | Q47155: 1ok7 1unn 4ir1 4ir9 4ird 4irk 4q43 4q44 4q45 4r8u 5c5j

(-) Related Entries Specified in the PDB File

4ir1 4ir9 4irk