Domain ID e2dy4B4

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  • A: mixed a+b and a/b
  • X: Ribonuclease H-like
  • H: Ribonuclease H-like
  • T: Ribonuclease H-like
  • F: DNA_pol_B_exo1
UID: 000115115
Type: Automatic domain
Parent: e1ih7A4
Range: B:1-375
PDB: 2dy4
PDB Description: DNA polymerase
UniProt: Q38087
Species: Enterobacteria phage RB69

Structure of domain e2dy4B4

Domains in the same chain:

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e2dy4B4 B:1-375 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e2dy4B3 B:376-467,B:574-731 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e2dy4B1 B:468-573 "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I
e2dy4B2 B:732-902 "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I

Domains in the same PDB:

e2dy4A4 A:1-375 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e2dy4A3 A:376-467,A:574-731 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e2dy4A1 A:468-573 "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I
e2dy4A2 A:732-902 "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I
e2dy4B4 B:1-375 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e2dy4B3 B:376-467,B:574-731 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e2dy4B1 B:468-573 "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I
e2dy4B2 B:732-902 "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I
e2dy4C4 C:1-375 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e2dy4C3 C:376-467,C:574-731 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e2dy4C1 C:468-573 "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I
e2dy4C2 C:732-900 "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I
e2dy4D4 D:1-375 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e2dy4D3 D:376-467,D:574-731 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e2dy4D1 D:468-573 "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I "fingers" domain in bacteriophage RB69-like DNA polymerase I
e2dy4D2 D:732-897 "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I "thumb" domain in bacteriophage RB69-like DNA polymerase I

Structural contacts of domain e2dy4B4 of H-group "Ribonuclease H-like":

The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain IDSymmetry operatorH-groupVisualization
e2dy4A4 B:x,y,z->A:X-1,Y,Z Ribonuclease H-like Interaction Interface Pymol
e2dy4C2 B:X,Y-1,Z->C:x,y,z "thumb" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol
e2dy4D2 B:x,y,z->D:X-1,Y,Z "thumb" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol
e2dy4D1 B:-X,Y-1/2,-Z->D:x,y,z "fingers" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol