Protein profile

KP13_00050

DNA replication and repair protein recF

Genome: KpKP13

Gene: AHE41974.1 recF Structure source: AlphaFold + ColabFold UniProt A0A0H3H4V2
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Amino acids 357
Annotations 8
Features 18
PDB binders 1
Druggability 0.812

Overview

Basic information about this protein and its source genome.

Accession
KP13_00050
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE41974.1 recF
Status
annotated
Amino acids
357
Structure source
AlphaFold + ColabFold
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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:0003697 Binding to single-stranded DNA. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GO:0000731 Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.118
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.83

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 0.812
Structure A0A0H3H4V2
Pocket Pocket 2
P2Rank 0.864
Structure A0A0H3H4V2
Pocket Pocket 1
ColabFold model
FPocket 0.401 · Pocket 17
P2Rank 0.867 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 145 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0003697 Binding to single-stranded DNA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0000731 Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
  • GO:0006302 The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
3 354 Pfam PF02463 RecF/RecN/SMC N terminal domain
3 354 InterPro IPR003395 RecF/RecN/SMC, N-terminal
1 356 PANTHER PTHR32182 DNA REPLICATION AND REPAIR PROTEIN RECF
298 316 ProSitePatterns PS00618 RecF protein signature 2.
298 316 InterPro IPR018078 DNA-binding, RecF, conserved site
1 343 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 343 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
117 137 ProSitePatterns PS00617 RecF protein signature 1.
117 137 InterPro IPR018078 DNA-binding, RecF, conserved site
120 297 Gene3D G3DSA:1.20.1050.90 -
120 297 InterPro IPR042174 DNA-binding RecF, domain 2
120 297 FunFam G3DSA:1.20.1050.90:FF:000001 DNA replication and repair protein RecF
6 331 Gene3D G3DSA:3.40.50.300 -
6 331 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 357 Hamap MF_00365 DNA replication and repair protein RecF [recF].
1 357 InterPro IPR001238 DNA-binding, RecF
1 355 NCBIfam TIGR00611 DNA replication and repair protein RecF
1 355 InterPro IPR001238 DNA-binding, RecF

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_A0A0H3H4V2
AlphaFold — — full sequence — Viewing
ColabFold KP13_00050
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
2 0.812

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 19.34 0.838
2 2.16 0.051
3 1.86 0.036

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
AGS
5Z69
Q8RDL3 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.