General information
PDB ID 2DY4
Title CRYSTAL STRUCTURE OF RB69 GP43 IN COMPLEX WITH DNA CONTAINING THYMINE GLYCOL
PDB header TRANSFERASE/DNA
Date 2006-09-06
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.65
Kind dna
Organism ENTEROBACTERIA PHAGE RB69
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb2dy4.pdb ABCD EFGHIJKL 0
Biounits:
2dy4.pdb1.pdb A EF 1
2dy4.pdb2.pdb B GH 1
2dy4.pdb3.pdb C IJ 1
2dy4.pdb4.pdb D KL 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
DNA_pol_B_exo1 Family Q38087_19-293 6e-23 1 CL0219 A 87 293 F  L-Bb 
DNA_pol_B Family Q38087_363-784 6.5e-23 1 CL0194 A 362 657 EF  S-Bb L-Bb L-Mn 
DNA_pol_B Family Q38087_363-784 1.2e-23 1 CL0194 B 362 658 GH  H-Bb S-Bb L-Bb L-Mn 
DNA_pol_B_exo1 Family Q38087_19-293 4.9e-23 1 CL0219 B 87 293 GH  L-Bb 
DNA_pol_B_exo1 Family Q38087_19-293 5.5e-23 1 CL0219 C 87 293 IJ  L-Bb 
DNA_pol_B Family Q38087_363-784 6.5e-23 1 CL0194 C 362 657 IJ  H-Bb S-Bb L-Bb 
DNA_pol_B Family Q38087_363-784 6.4e-23 1 CL0194 D 362 657 KL  S-Bb L-Bb 
DNA_pol_B_exo1 Family Q38087_19-293 5.2e-20 1 CL0219 D 87 293   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: DnaQ-like 3'-5' exonuclease
Exonuclease domain of family B DNA polymerases A 1 375 EF  L-Bb 
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: DnaQ-like 3'-5' exonuclease
Exonuclease domain of family B DNA polymerases B 1 375 GH  L-Bb 
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: DnaQ-like 3'-5' exonuclease
Exonuclease domain of family B DNA polymerases C 1 375 IJ  L-Bb 
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: DnaQ-like 3'-5' exonuclease
Exonuclease domain of family B DNA polymerases D 1 375 K -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
Family B DNA polymerase A 376 902 EF -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
Family B DNA polymerase B 376 902 GH -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
Family B DNA polymerase C 376 900 IJ -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
Family B DNA polymerase D 376 897 KL -
GO terms
Protein chains: GO type: GO description:
A/B/C/D=1-903 F 3'-5' exonuclease activity
A/B/C/D=1-903 F DNA binding
A/B/C/D=1-903 F DNA-directed DNA polymerase activity
A/B/C/D=1-903 F metal ion binding
A/B/C/D=1-903 F nucleotide binding
A/B/C/D=1-903 P bidirectional double-stranded viral DNA replication
A/B/C/D=1-903 P DNA replication
Sequences
Download file with secondary structure created by Stride  
2dy4.pdb1.pdb:   [ download sequences in FASTA format ]
E (dna): 
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F (dna): 
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A (protein): 
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2dy4.pdb2.pdb:   [ download sequences in FASTA format ]
G (dna): 
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H (dna): 
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B (protein): 
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2dy4.pdb3.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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C (protein): 
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2dy4.pdb4.pdb:   [ download sequences in FASTA format ]
K (dna): 
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L (dna): 
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D (protein): 
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