Protein profile

VK055_2801

bacterial regulatory, gntR family protein

Genome: KpATCC43816

Gene: AIK81390.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQW0
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Amino acids 241
Annotations 4
Features 26
PDB binders 2
Druggability 0.286

Overview

Basic information about this protein and its source genome.

Accession
VK055_2801
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81390.1
Status
annotated
Amino acids
241
Structure source
AlphaFold + ColabFold
GO
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

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 (%)
31.69
Localization
Cytoplasmic
ColabFold pLDDT
88.37

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 0.286
Structure A0A0H3GQW0
Pocket Pocket 13
P2Rank 0.389
Structure A0A0H3GQW0
Pocket Pocket 1
ColabFold model
FPocket 0.826 · Pocket 3
P2Rank 0.454 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 10 / 4744 genomes with a hit
Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
6 82 FunFam G3DSA:1.10.10.10:FF:000079 GntR family transcriptional regulator
80 241 Gene3D G3DSA:3.40.1410.10 -
80 241 InterPro IPR028978 Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
18 77 SMART SM00345 gntr3
18 77 InterPro IPR000524 Transcription regulator HTH, GntR
97 238 SMART SM00866 UTRA_2
97 238 InterPro IPR011663 UbiC transcription regulator-associated
9 240 PANTHER PTHR44846 MANNOSYL-D-GLYCERATE TRANSPORT/METABOLISM SYSTEM REPRESSOR MNGR-RELATED
12 80 ProSiteProfiles PS50949 GntR-type HTH domain profile.
12 80 InterPro IPR000524 Transcription regulator HTH, GntR
65 240 SUPERFAMILY SSF64288 Chorismate lyase-like
65 240 InterPro IPR028978 Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
37 51 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
37 51 InterPro IPR000524 Transcription regulator HTH, GntR
51 67 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
51 67 InterPro IPR000524 Transcription regulator HTH, GntR
2 78 Gene3D G3DSA:1.10.10.10 -
2 78 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
106 237 Pfam PF07702 UTRA domain
106 237 InterPro IPR011663 UbiC transcription regulator-associated
13 78 CDD cd07377 WHTH_GntR
13 78 InterPro IPR000524 Transcription regulator HTH, GntR
9 93 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
9 93 InterPro IPR036390 Winged helix DNA-binding domain superfamily
14 77 Pfam PF00392 Bacterial regulatory proteins, gntR family
14 77 InterPro IPR000524 Transcription regulator HTH, GntR

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_A0A0H3GQW0
AlphaFold — — full sequence — Viewing
ColabFold VK055_2801
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
7 0.036
1 0.004
12 0.004
17 0.0

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 8.56 0.389
2 2.85 0.072
3 2.66 0.064
4 0.91 0.004

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.

2 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
3VV
4PDK
Q9KQU8 1032.0 Da LogP 4.70 TPSA 363.6 3 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H…
FLC
3CNV
A0A0H3LYW6 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[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.