Protein profile

KP13_05170

Endonuclease III

Genome: KpKP13

Gene: nth AHE44289.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTN3
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Amino acids 211
Annotations 11
Features 29
PDB binders 1
Druggability 0.425

Overview

Basic information about this protein and its source genome.

Accession
KP13_05170
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nth AHE44289.1
Status
annotated
Amino acids
211
Structure source
AlphaFold + ColabFold
EC
4.2.99.18
GO
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER). GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. 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: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 (%)
35.484
Human E-value
4.82e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
83.254
DEG E-value
1.21e-130
Localization
Cytoplasmic
ColabFold pLDDT
97.48

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 0.425
Structure A0A0H3GTN3
Pocket Pocket 1
P2Rank 0.639
Structure A0A0H3GTN3
Pocket Pocket 1
ColabFold model
FPocket 0.414 · Pocket 1
P2Rank 0.6 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 376 / 4744 genomes with a hit
Normalized 0.079

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
  • GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0140078 Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate.
  • GO:0019104 Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
  • GO:0046872 Binding to a metal ion.
  • GO:0006285 The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
21 132 FunFam G3DSA:1.10.340.30:FF:000001 Endonuclease III
187 203 Pfam PF10576 Iron-sulfur binding domain of endonuclease III
187 203 InterPro IPR003651 Endonuclease III-like, iron-sulphur cluster loop motif
12 205 Gene3D G3DSA:1.10.1670.10 -
12 205 InterPro IPR023170 Helix-hairpin-helix, base-excision DNA repair, C-terminal
186 206 SMART SM00525 ccc3
186 206 InterPro IPR003651 Endonuclease III-like, iron-sulphur cluster loop motif
2 208 PANTHER PTHR10359 A/G-SPECIFIC ADENINE GLYCOSYLASE/ENDONUCLEASE III
21 132 Gene3D G3DSA:1.10.340.30 Hypothetical protein; domain 2
1 209 Hamap MF_00942 Endonuclease III [nth].
1 209 InterPro IPR005759 Endonuclease III
30 183 CDD cd00056 ENDO3c
30 183 InterPro IPR003265 HhH-GPD domain
100 127 Pfam PF00633 Helix-hairpin-helix motif
100 127 InterPro IPR000445 Helix-hairpin-helix motif
34 168 Pfam PF00730 HhH-GPD superfamily base excision DNA repair protein
34 168 InterPro IPR003265 HhH-GPD domain
3 207 SUPERFAMILY SSF48150 DNA-glycosylase
3 207 InterPro IPR011257 DNA glycosylase
38 185 SMART SM00478 endo3end
38 185 InterPro IPR003265 HhH-GPD domain
1 210 PIRSF PIRSF001435 Nth
187 203 ProSitePatterns PS00764 Endonuclease III iron-sulfur binding region signature.
187 203 InterPro IPR004035 Endonuclease III, iron-sulphur binding site
127 205 FunFam G3DSA:1.10.1670.10:FF:000001 Endonuclease III
4 194 NCBIfam TIGR01083 endonuclease III
4 194 InterPro IPR005759 Endonuclease III
102 131 ProSitePatterns PS01155 Endonuclease III family signature.
102 131 InterPro IPR004036 Endonuclease III-like, conserved site-2

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_A0A0H3GTN3
AlphaFold — — full sequence — Viewing
ColabFold KP13_05170
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 0.425

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 8.57 0.458
2 2.39 0.063

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.

5 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
ADE
1MUD
P17802 135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N

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.