General information
PDB ID 2PYJ
Title PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA AND INCOMING NUCLEOTIDE SUBSTRATES (TERNARY COMPLEX)
PDB header REPLICATION, TRANSFERASE/DNA
Date 2007-05-16
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.03
Kind dna
Organism BACILLUS PHAGE PHI29
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
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Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb2pyj.pdb AB XYQRKJ 0
Biounits:
2pyj.pdb1.pdb A XY 1
2pyj.pdb2.pdb B QR 1
2pyj.pdb3.pdb KJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
DNA_pol_B_2 Family P03680_49-477 4.4e-99 1 CL0194 A 49 477 XY   
DNA_pol_B_2 Family P03680_49-477 4.5e-99 1 CL0194 B 49 477 RQ   
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 phi29 DNA polymerase A 5 187 XY  H-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 phi29 DNA polymerase A 5 187 XY -
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 phi29 DNA polymerase A 5 187  H-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 phi29 DNA polymerase A 5 187 -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
phi29 DNA polymerase A 188 575 XY -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
phi29 DNA polymerase A 188 575 -
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 phi29 DNA polymerase B 5 187 RQ  L-Mj 
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 phi29 DNA polymerase B 5 187 RQ -
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 phi29 DNA polymerase B 5 187  L-Mj 
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 phi29 DNA polymerase B 5 187 -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
phi29 DNA polymerase B 188 575 QR -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: DNA polymerase I
phi29 DNA polymerase B 188 575 -
GO terms
Protein chains: GO type: GO description:
A/B=1-575 F nucleoside binding
A/B=1-575 F 3'-5' exonuclease activity
A/B=1-575 F nucleotide binding
A/B=1-575 F DNA binding
A/B=1-575 F DNA-directed DNA polymerase activity
A/B=1-575 P nucleic acid phosphodiester bond hydrolysis
A/B=1-575 P DNA replication
Sequences
Download file with secondary structure created by Stride  
2pyj.pdb1.pdb:   [ download sequences in FASTA format ]
X (dna): 
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Y (dna): 
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A (protein): 
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2pyj.pdb2.pdb:   [ download sequences in FASTA format ]
Q (dna): 
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R (dna): 
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B (protein): 
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2pyj.pdb3.pdb:   [ download sequences in FASTA format ]
J (dna): 
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K (dna): 
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