Protein profile

VK055_2180

exodeoxyribonuclease VII, small subunit

Genome: KpATCC43816

Gene: AIK80785.1 xseB Structure source: AlphaFold + ColabFold UniProt A0A0H3GP02
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Amino acids 80
Annotations 5
Features 16
PDB binders 0
Druggability 0.394

Overview

Basic information about this protein and its source genome.

Accession
VK055_2180
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80785.1 xseB
Status
annotated
Amino acids
80
Structure source
AlphaFold + ColabFold
EC
3.1.11.6
GO
GO:0009318 An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA. GO:0006308 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GO:0008855 Catalysis of the exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield 5'-phosphomononucleotides. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
83.75
DEG E-value
1.79e-43
Localization
Cytoplasmic
ColabFold pLDDT
85.0

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.394
Structure A0A0H3GP02
Pocket Pocket 2
P2Rank
Structure A0A0H3GP02
Pocket No pockets
ColabFold model
FPocket 0.64 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 4744 genomes with a hit
Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009318 An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA.
  • GO:0006308 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
  • GO:0008855 Catalysis of the exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield 5'-phosphomononucleotides.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
5 79 FunFam G3DSA:1.10.287.1040:FF:000001 Exodeoxyribonuclease 7 small subunit
3 74 SUPERFAMILY SSF116842 XseB-like
3 74 InterPro IPR037004 Exonuclease VII, small subunit superfamily
1 80 PIRSF PIRSF006488 ExoVII_small
1 80 InterPro IPR003761 Exonuclease VII, small subunit
5 79 Gene3D G3DSA:1.10.287.1040 Exonuclease VII, small subunit
5 79 InterPro IPR037004 Exonuclease VII, small subunit superfamily
1 78 PANTHER PTHR34137 EXODEOXYRIBONUCLEASE 7 SMALL SUBUNIT
1 78 InterPro IPR003761 Exonuclease VII, small subunit
46 66 Coils Coil Coil
10 65 NCBIfam TIGR01280 exodeoxyribonuclease VII small subunit
10 65 InterPro IPR003761 Exonuclease VII, small subunit
10 70 Hamap MF_00337 Exodeoxyribonuclease 7 small subunit [xseB].
10 70 InterPro IPR003761 Exonuclease VII, small subunit
11 62 Pfam PF02609 Exonuclease VII small subunit
11 62 InterPro IPR003761 Exonuclease VII, small subunit

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GP02
AlphaFold — — full sequence — Viewing
ColabFold VK055_2180
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.394
7 0.009
1 0.003
5 0.0