Protein profile

VK055_0018

DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway

Genome: KpATCC43816

Gene: AIK78648.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVL1
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Amino acids 164
Annotations 4
Features 11
PDB binders 0
Druggability 0.292

Overview

Basic information about this protein and its source genome.

Accession
VK055_0018
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78648.1
Status
annotated
Amino acids
164
Structure source
AlphaFold + ColabFold
EC
3.1.-.-
GO
GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination. GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

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 (%)
36.066
Localization
Cytoplasmic
ColabFold pLDDT
91.25

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 0.292
Structure A0A0H3GVL1
Pocket Pocket 4
P2Rank 0.792
Structure A0A0H3GVL1
Pocket Pocket 1
ColabFold model
FPocket 0.615 · Pocket 9
P2Rank 0.794 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 76 / 4744 genomes with a hit
Normalized 0.016

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
1 151 PIRSF PIRSF018267 VSR_endonuc
1 151 InterPro IPR004603 DNA mismatch endonuclease VSR
5 137 CDD cd00221 Vsr
5 137 InterPro IPR004603 DNA mismatch endonuclease VSR
21 156 Gene3D G3DSA:3.40.960.10 VSR Endonuclease
2 153 SUPERFAMILY SSF52980 Restriction endonuclease-like
2 153 InterPro IPR011335 Restriction endonuclease type II-like
1 118 NCBIfam TIGR00632 DNA mismatch endonuclease Vsr
1 118 InterPro IPR004603 DNA mismatch endonuclease VSR
2 74 Pfam PF03852 DNA mismatch endonuclease Vsr
2 74 InterPro IPR004603 DNA mismatch endonuclease VSR

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_A0A0H3GVL1
AlphaFold — — full sequence — Viewing
ColabFold VK055_0018
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
4 0.292
12 0.263

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 12.92 0.667
2 2.02 0.044
3 1.71 0.03
4 1.11 0.008