Protein profile

KP13_04416

putative endonuclease 4

Genome: KpKP13

Gene: nfo AHE43565.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQY5
Export view
Amino acids 277
Annotations 8
Features 24
PDB binders 1
Druggability 0.69

Overview

Basic information about this protein and its source genome.

Accession
KP13_04416
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nfo AHE43565.1
Status
annotated
Amino acids
277
Structure source
AlphaFold + ColabFold
EC
3.1.21.2
GO
GO:0008270 Binding to a zinc ion (Zn). 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:0008833 Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. 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:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.54

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 0.69
Structure A0A0H3GQY5
Pocket Pocket 1
P2Rank 0.755
Structure A0A0H3GQY5
Pocket Pocket 1
ColabFold model
FPocket 0.612 · Pocket 1
P2Rank 0.87 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 480 / 4744 genomes with a hit
Normalized 0.101

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:0008270 Binding to a zinc ion (Zn).
  • 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:0008833 Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
  • 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:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
13 270 Pfam PF01261 Xylose isomerase-like TIM barrel
13 270 InterPro IPR013022 Xylose isomerase-like, TIM barrel domain
62 70 ProSitePatterns PS00729 AP endonucleases family 2 signature 1.
62 70 InterPro IPR018246 AP endonuclease 2, zinc binding site
168 175 ProSitePatterns PS00730 AP endonucleases family 2 signature 2.
168 175 InterPro IPR018246 AP endonuclease 2, zinc binding site
1 277 Gene3D G3DSA:3.20.20.150 -
1 273 ProSiteProfiles PS51432 AP endonucleases family 2 profile.
1 273 InterPro IPR001719 AP endonuclease 2
1 270 PANTHER PTHR21445 ENDONUCLEASE IV ENDODEOXYRIBONUCLEASE IV
1 270 InterPro IPR001719 AP endonuclease 2
208 224 ProSitePatterns PS00731 AP endonucleases family 2 signature 3.
208 224 InterPro IPR018246 AP endonuclease 2, zinc binding site
1 269 NCBIfam TIGR00587 deoxyribonuclease IV
1 269 InterPro IPR001719 AP endonuclease 2
2 270 SUPERFAMILY SSF51658 Xylose isomerase-like
2 270 InterPro IPR036237 Xylose isomerase-like superfamily
2 269 CDD cd00019 AP2Ec
2 269 InterPro IPR001719 AP endonuclease 2
1 272 SMART SM00518 ap2real3
1 272 InterPro IPR001719 AP endonuclease 2
1 277 FunFam G3DSA:3.20.20.150:FF:000001 Probable endonuclease 4
2 272 Hamap MF_00152 Probable endonuclease 4 [nfo].
2 272 InterPro IPR001719 AP endonuclease 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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GQY5
AlphaFold — — full sequence — Viewing
ColabFold KP13_04416
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 0.69

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 7.99 0.425
2 6.81 0.349
3 2.72 0.082
4 1.82 0.034
5 1.7 0.029

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.

115 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
CAC
3AAL
Q5KX27 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[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.