Protein profile

VK055_4362

5'-3' exonuclease, C-terminal SAM fold family protein

Genome: KpATCC43816

Gene: AIK82905.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWW8
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Amino acids 251
Annotations 9
Features 25
PDB binders 2
Druggability 0.538

Overview

Basic information about this protein and its source genome.

Accession
VK055_4362
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82905.1
Status
annotated
Amino acids
251
Structure source
AlphaFold + ColabFold
EC
3.1.-.-
GO
GO:0017108 Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. 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:0033567 The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand. GO:0048256 Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0008409 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.

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 (%)
34.286
Localization
Cytoplasmic
ColabFold pLDDT
95.71

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 0.538
Structure A0A0H3GWW8
Pocket Pocket 8
P2Rank 0.877
Structure A0A0H3GWW8
Pocket Pocket 1
ColabFold model
FPocket 0.423 · Pocket 3
P2Rank 0.84 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 117 / 4744 genomes with a hit
Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0017108 Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
  • 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:0033567 The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
  • GO:0048256 Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0008409 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0030955 Binding to a potassium ion (K+).

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
190 210 Coils Coil Coil
162 251 FunFam G3DSA:1.10.150.20:FF:000003 DNA polymerase I
162 234 CDD cd09898 H3TH_53EXO
162 234 InterPro IPR020045 DNA polymerase I-like, H3TH domain
4 240 PANTHER PTHR42646 FLAP ENDONUCLEASE XNI
4 240 InterPro IPR038969 Flap endonuclease
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
160 250 Pfam PF01367 5'-3' exonuclease, C-terminal SAM fold
160 250 InterPro IPR020045 DNA polymerase I-like, H3TH domain
2 251 Hamap MF_01192 Flap endonuclease Xni [xni].
2 251 InterPro IPR022895 Flap endonuclease Xni
1 161 Gene3D G3DSA:3.40.50.1010 -
162 197 SMART SM00279 HhH_4
162 197 InterPro IPR008918 Helix-hairpin-helix motif, class 2
162 251 Gene3D G3DSA:1.10.150.20 -
160 243 SUPERFAMILY SSF47807 5' to 3' exonuclease, C-terminal subdomain
160 243 InterPro IPR036279 5'-3' exonuclease, C-terminal domain superfamily
4 159 SUPERFAMILY SSF88723 PIN domain-like
4 159 InterPro IPR029060 PIN-like domain superfamily
7 154 CDD cd09859 PIN_53EXO
1 161 FunFam G3DSA:3.40.50.1010:FF:000011 Flap endonuclease Xni
3 250 SMART SM00475 53exo3
3 250 InterPro IPR002421 5'-3' exonuclease
5 151 Pfam PF02739 5'-3' exonuclease, N-terminal resolvase-like domain
5 151 InterPro IPR020046 5'-3' exonuclease, alpha-helical arch, N-terminal

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_A0A0H3GWW8
AlphaFold — — full sequence — Viewing
ColabFold VK055_4362
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
8 0.538
1 0.364

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 16.52 0.78
2 2.14 0.05
3 1.48 0.021
4 1.0 0.006

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.

15 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
B3P
5HML
P06229 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
PIV
3ZDA
Q8X6R9 102.1 Da LogP 1.12 TPSA 37.3 ✓ Ro5 ✓ Clean CC(C)(C)C(=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.