Protein profile

VK055_1238

exodeoxyribonuclease III

Genome: KpATCC43816

Gene: AIK79861.1 xth Structure source: AlphaFold + ColabFold UniProt A0A235PVE3
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Amino acids 268
Annotations 8
Features 20
PDB binders 1
Druggability 0.186

Overview

Basic information about this protein and its source genome.

Accession
VK055_1238
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79861.1 xth
Status
annotated
Amino acids
268
Structure source
AlphaFold + ColabFold
EC
3.1.11.2
GO
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.172
Human E-value
6.47e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
72.285
DEG E-value
1.04e-148
Localization
Cytoplasmic
ColabFold pLDDT
97.02

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 0.186
Structure A0A235PVE3
Pocket Pocket 1
P2Rank 0.736
Structure A0A235PVE3
Pocket Pocket 1
ColabFold model
FPocket 0.599 · Pocket 10
P2Rank 0.824 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 151 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 268 ProSiteProfiles PS51435 AP endonucleases family 1 profile.
1 268 InterPro IPR004808 AP endonuclease 1
1 266 NCBIfam TIGR00195 exodeoxyribonuclease III
1 268 FunFam G3DSA:3.60.10.10:FF:000006 Exodeoxyribonuclease III
1 267 SUPERFAMILY SSF56219 DNase I-like
1 267 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 266 CDD cd09086 ExoIII-like_AP-endo
1 266 InterPro IPR037493 Exodeoxyribonuclease III-like
223 234 ProSitePatterns PS00728 AP endonucleases family 1 signature 3.
223 234 InterPro IPR020848 AP endonuclease 1, conserved site
1 268 Gene3D G3DSA:3.60.10.10 Endonuclease/exonuclease/phosphatase
1 268 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 267 PANTHER PTHR43250 -
1 267 InterPro IPR037493 Exodeoxyribonuclease III-like
4 259 Pfam PF03372 Endonuclease/Exonuclease/phosphatase family
4 259 InterPro IPR005135 Endonuclease/exonuclease/phosphatase
27 36 ProSitePatterns PS00726 AP endonucleases family 1 signature 1.
27 36 InterPro IPR020847 AP endonuclease 1, binding site
1 266 NCBIfam TIGR00633 exodeoxyribonuclease III
1 266 InterPro IPR004808 AP endonuclease 1

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_A0A235PVE3
AlphaFold — — full sequence — Viewing
ColabFold VK055_1238
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 12.24 0.644
2 1.48 0.02
3 1.33 0.015
4 1.07 0.007

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

151 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
PGA
5WN2
P27695 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.