Protein profile

KP13_01622

Crossover junction endodeoxyribonuclease ruvC

Genome: KpKP13

Gene: AHE43855.1 ruvC Structure source: AlphaFold + ColabFold UniProt A0A0H3GVH0
Export view
Amino acids 173
Annotations 10
Features 27
PDB binders 0
Druggability 0.304

Overview

Basic information about this protein and its source genome.

Accession
KP13_01622
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43855.1 ruvC
Status
annotated
Amino acids
173
Structure source
AlphaFold + ColabFold
EC
3.1.21.10
GO
GO:0004520 Catalysis of the cleavage of ester linkages within deoxyribonucleic acid by creating internal breaks. GO:0003676 Binding to a nucleic acid. GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. 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:0008821 Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 (%)
97.11
DEG E-value
4.08e-123
Localization
Cytoplasmic
ColabFold pLDDT
91.05

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 0.304
Structure A0A0H3GVH0
Pocket Pocket 2
P2Rank 0.198
Structure A0A0H3GVH0
Pocket Pocket 1
ColabFold model
FPocket 0.49 · Pocket 9
P2Rank 0.205 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 208 / 4744 genomes with a hit
Normalized 0.044

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0004520 Catalysis of the cleavage of ester linkages within deoxyribonucleic acid by creating internal breaks.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • 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:0008821 Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0048476 An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
4 136 CDD cd16962 RuvC
4 136 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
2 159 Gene3D G3DSA:3.30.420.10 -
2 159 InterPro IPR036397 Ribonuclease H superfamily
4 157 NCBIfam TIGR00228 crossover junction endodeoxyribonuclease RuvC
4 157 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
4 150 Pfam PF02075 Crossover junction endodeoxyribonuclease RuvC
4 150 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
3 156 SUPERFAMILY SSF53098 Ribonuclease H-like
3 156 InterPro IPR012337 Ribonuclease H-like superfamily
2 153 Hamap MF_00034 Crossover junction endodeoxyribonuclease RuvC [ruvC].
2 153 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
3 162 PANTHER PTHR30194 CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC
3 162 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
5 18 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
5 18 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
61 77 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
61 77 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
107 126 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
107 126 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
138 150 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
138 150 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
83 99 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
83 99 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
2 158 FunFam G3DSA:3.30.420.10:FF:000002 Crossover junction endodeoxyribonuclease RuvC
113 147 ProSitePatterns PS01321 Crossover junction endodeoxyribonuclease ruvC signature.
113 147 InterPro IPR020563 Crossover junction endodeoxyribonuclease RuvC, magnesium-binding 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

Loading 3D structure...

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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_A0A0H3GVH0
AlphaFold — — full sequence — Viewing
ColabFold KP13_01622
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 0.304
1 0.224
5 0.224

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 3.41 0.122