Domain ID e3ikmD5

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  • A: alpha bundles
  • X: "fingers" domain in bacteriophage RB69-like DNA polymerase I
  • H: "fingers" domain in bacteriophage RB69-like DNA polymerase I
  • T: "fingers" domain in bacteriophage RB69-like DNA polymerase I
  • F: Unmapped domains
UID: 001187778
Type: Automatic domain
Parent: e2hhvA2
Range: D:416-673,D:710-879
PDB: 3ikm
PDB Description: DNA polymerase subunit gamma-1
UniProt: P54098
Hsap BLAST neighbor: P54098
Species: Homo sapiens

Structure of domain e3ikmD5

Domains in the same chain:

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e3ikmD8 D:70-318,D:345-415 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e3ikmD5 D:416-673,D:710-879 "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
e3ikmD7 D:880-908,D:1081-1239 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e3ikmD6 D:909-1080 helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I

Domains in the same PDB:

e3ikmA1 A:70-417 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e3ikmA2 A:418-881 "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
e3ikmA3 A:882-910,A:1098-1239 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e3ikmA4 A:911-1097 helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I
e3ikmB3 B:67-137,B:179-356 Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases
e3ikmB2 B:369-485 Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS
e3ikmC5 C:59-146,C:178-359 Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases
e3ikmC6 C:360-485 Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS
e3ikmD8 D:70-318,D:345-415 Ribonuclease H-like Ribonuclease H-like Ribonuclease H-like
e3ikmD5 D:416-673,D:710-879 "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
e3ikmD7 D:880-908,D:1081-1239 Alpha-beta plaits Adenylyl and guanylyl cyclase catalytic domain-like Adenylyl and guanylyl cyclase catalytic domain-like
e3ikmD6 D:909-1080 helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I helical bundle in Bacillus stearothermophilus-like DNA polymerase I
e3ikmE3 E:67-137,E:179-356 Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases
e3ikmE2 E:369-485 Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS
e3ikmF5 F:59-146,F:178-356 Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases Class II aaRS and biotin synthetases
e3ikmF6 F:357-485 Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS Anticodon-binding domain of Class II aaRS

Structural contacts of domain e3ikmD5 of H-group ""fingers" domain in bacteriophage RB69-like DNA polymerase I":

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
e3ikmF6 D:X,Y,Z->F:x,y,z Anticodon-binding domain of Class II aaRS Interaction Interface Pymol
e3ikmF5 D:X,Y,Z->F:x,y,z Class II aaRS and biotin synthetases Interaction Interface Pymol
e3ikmA2 D:X,Y-1,Z->A:x,y,z "fingers" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol
e3ikmA1 D:X,Y-1,Z->A:x,y,z Ribonuclease H-like Interaction Interface Pymol
e3ikmA4 D:X,Y-1,Z->A:x,y,z helical bundle in Bacillus stearothermophilus-like DNA polymerase I Interaction Interface Pymol
e3ikmA2 D:X-1,Y-1,Z->A:x,y,z "fingers" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol
e3ikmC5 D:-Y+3,X-Y-1,Z-1/3->C:x,y,z Class II aaRS and biotin synthetases Interaction Interface Pymol
e3ikmA2 D:-Y+2,X-Y-1,Z-1/3->A:x,y,z "fingers" domain in bacteriophage RB69-like DNA polymerase I Interaction Interface Pymol
e3ikmB3 D:-Y+2,X-Y-1,Z-1/3->B:x,y,z Class II aaRS and biotin synthetases Interaction Interface Pymol