Protein profile

VK055_2135

DNA base-flipping protein

Genome: KpATCC43816

Gene: AIK80740.1 ybaZ Structure source: ColabFold
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Amino acids 89
Annotations 2
Features 10
PDB binders 1
Druggability 0.683

Overview

Basic information about this protein and its source genome.

Accession
VK055_2135
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80740.1 ybaZ
Status
annotated
Amino acids
89
Structure source
ColabFold
GO
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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.681
Human E-value
7.97e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
46.429
DEG E-value
2.88e-18
Localization
Unknown
ColabFold pLDDT
94.44

Selected Druggability evidence

ColabFold / curated 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 0.683
Structure CB_VK055_2135
Pocket Pocket 4
P2Rank 0.003
Structure CB_VK055_2135
Pocket Pocket 1
ColabFold model
FPocket 0.683 · Pocket 4
P2Rank 0.003 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 113 / 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 GO

Gene Ontology (GO)

2
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
1 71 CDD cd06445 ATase
1 71 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
1 89 FunFam G3DSA:1.10.10.10:FF:000148 6-O-methylguanine DNA methyltransferase
2 72 Pfam PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
2 72 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
1 89 Gene3D G3DSA:1.10.10.10 -
1 89 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
2 88 PANTHER PTHR42942 6-O-METHYLGUANINE DNA METHYLTRANSFERASE
2 73 SUPERFAMILY SSF46767 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
2 73 InterPro IPR036217 Methylated DNA-protein cysteine methyltransferase, DNA binding domain

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
ColabFold VK055_2135
ColabFold — — full sequence — Viewing
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 0.683
1 0.043
5 0.003
7 0.001

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 0.9 0.003

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
PBO
3GYH
Q9UTN9 149.2 Da LogP 2.06 TPSA 30.0 ✓ Ro5 ✓ Clean CCCC(=O)c1cccnc1

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.