Protein profile

KP13_01737

Deoxyribonuclease tatD

Genome: KpKP13

Gene: AHE46960.1 tatD Structure source: AlphaFold + ColabFold UniProt A0A0H3GH78
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Amino acids 263
Annotations 8
Features 17
PDB binders 1
Druggability 0.007

Overview

Basic information about this protein and its source genome.

Accession
KP13_01737
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46960.1 tatD
Status
annotated
Amino acids
263
Structure source
AlphaFold + ColabFold
EC
3.1.11.- 3.1.13.-
GO
GO:0016788 Catalysis of the hydrolysis of any ester bond. GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0000287 Binding to a magnesium (Mg) ion. GO:0008310 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.364
Human E-value
3.42e-14
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.88

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 0.007
Structure A0A0H3GH78
Pocket Pocket 3
P2Rank 0.859
Structure A0A0H3GH78
Pocket Pocket 1
ColabFold model
FPocket 0.294 · Pocket 9
P2Rank 0.849 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0016788 Catalysis of the hydrolysis of any ester bond.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0008310 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 262 Gene3D G3DSA:3.20.20.140 -
1 259 Hamap MF_00901 3'-5' ssDNA/RNA exonuclease TatD [tatD].
1 259 InterPro IPR024918 3'-5' ssDNA/RNA exonuclease TatD
1 257 CDD cd01310 TatD_DNAse
1 257 InterPro IPR001130 3'-5' ssDNA/RNA exonuclease TatD-like
1 260 PIRSF PIRSF005902 DNase_TatD
1 260 InterPro IPR001130 3'-5' ssDNA/RNA exonuclease TatD-like
123 133 ProSitePatterns PS01090 TatD deoxyribonuclease family signature 2.
123 133 InterPro IPR018228 Deoxyribonuclease, TatD-related, conserved site
1 260 FunFam G3DSA:3.20.20.140:FF:000018 3'-5' ssDNA/RNA exonuclease TatD
1 258 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
1 258 InterPro IPR032466 Metal-dependent hydrolase
2 256 Pfam PF01026 TatD related DNase
2 256 InterPro IPR001130 3'-5' ssDNA/RNA exonuclease TatD-like
1 258 PANTHER PTHR46124 D-AMINOACYL-TRNA DEACYLASE
189 205 ProSitePatterns PS01091 TatD deoxyribonuclease family signature 3.
189 205 InterPro IPR018228 Deoxyribonuclease, TatD-related, conserved 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_A0A0H3GH78
AlphaFold — — full sequence — Viewing
ColabFold KP13_01737
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 16.73 0.786
2 1.39 0.017

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.

51 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
P33
1ZZM
P39408 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)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.