Protein profile

KP13_31948

exodeoxyribonuclease III

Genome: KpKP13

Gene: AHE45045.1 xthA Structure source: AlphaFold + ColabFold UniProt A0A0H3GLS9
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Amino acids 301
Annotations 6
Features 20
PDB binders 1
Druggability 0.438

Overview

Basic information about this protein and its source genome.

Accession
KP13_31948
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45045.1 xthA
Status
annotated
Amino acids
301
Structure source
AlphaFold + ColabFold
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: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:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule. GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.333
Human E-value
3.39e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
72.285
DEG E-value
2.5700000000000002e-148
Localization
Cytoplasmic
ColabFold pLDDT
90.4

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 0.438
Structure A0A0H3GLS9
Pocket Pocket 1
P2Rank 0.726
Structure A0A0H3GLS9
Pocket Pocket 1
ColabFold model
FPocket 0.519 · Pocket 3
P2Rank 0.664 · 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.

6 GO

Gene Ontology (GO)

6
  • 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: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:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
  • GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
34 301 Gene3D G3DSA:3.60.10.10 Endonuclease/exonuclease/phosphatase
34 301 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
34 299 CDD cd09086 ExoIII-like_AP-endo
34 299 InterPro IPR037493 Exodeoxyribonuclease III-like
37 292 Pfam PF03372 Endonuclease/Exonuclease/phosphatase family
37 292 InterPro IPR005135 Endonuclease/exonuclease/phosphatase
33 300 PANTHER PTHR43250 -
33 300 InterPro IPR037493 Exodeoxyribonuclease III-like
34 299 NCBIfam TIGR00633 exodeoxyribonuclease III
34 299 InterPro IPR004808 AP endonuclease 1
34 301 FunFam G3DSA:3.60.10.10:FF:000006 Exodeoxyribonuclease III
34 300 SUPERFAMILY SSF56219 DNase I-like
34 300 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
34 301 ProSiteProfiles PS51435 AP endonucleases family 1 profile.
34 301 InterPro IPR004808 AP endonuclease 1
34 299 NCBIfam TIGR00195 exodeoxyribonuclease III
256 267 ProSitePatterns PS00728 AP endonucleases family 1 signature 3.
256 267 InterPro IPR020848 AP endonuclease 1, conserved site
60 69 ProSitePatterns PS00726 AP endonucleases family 1 signature 1.
60 69 InterPro IPR020847 AP endonuclease 1, binding site

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_A0A0H3GLS9
AlphaFold — — full sequence — Viewing
ColabFold KP13_31948
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
1 0.438

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 11.18 0.599
2 1.53 0.022

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.