Protein profile

KP13_02266

Transcriptional activator protein lysR

Genome: KpKP13

Gene: lysR AHE42839.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXX4
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Amino acids 308
Annotations 5
Features 21
PDB binders 6
Druggability 0.041

Overview

Basic information about this protein and its source genome.

Accession
KP13_02266
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
lysR AHE42839.1
Status
annotated
Amino acids
308
Structure source
AlphaFold + ColabFold
GO
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. 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:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. GO:0010628 Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).

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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
92.04

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 0.041
Structure A0A0H3GXX4
Pocket Pocket 12
P2Rank 0.77
Structure A0A0H3GXX4
Pocket Pocket 1
ColabFold model
FPocket 0.285 · Pocket 16
P2Rank 0.694 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
  • GO:0010628 Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
93 298 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
96 297 Gene3D G3DSA:3.40.190.290 -
3 84 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
3 84 InterPro IPR036390 Winged helix DNA-binding domain superfamily
1 303 PANTHER PTHR30427 TRANSCRIPTIONAL ACTIVATOR PROTEIN LYSR
92 294 Pfam PF03466 LysR substrate binding domain
92 294 InterPro IPR005119 LysR, substrate-binding
3 87 FunFam G3DSA:1.10.10.10:FF:000174 LysR family transcriptional regulator
1 86 Gene3D G3DSA:1.10.10.10 -
1 86 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
6 64 Pfam PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
6 64 InterPro IPR000847 Transcription regulator HTH, LysR
4 61 ProSiteProfiles PS50931 LysR-type HTH domain profile.
4 61 InterPro IPR000847 Transcription regulator HTH, LysR
32 42 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
32 42 InterPro IPR000847 Transcription regulator HTH, LysR
42 53 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
42 53 InterPro IPR000847 Transcription regulator HTH, LysR
21 32 PRINTS PR00039 LysR bacterial regulatory protein HTH signature
21 32 InterPro IPR000847 Transcription regulator HTH, LysR
96 297 FunFam G3DSA:3.40.190.290:FF:000007 LysR family transcriptional regulator

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_A0A0H3GXX4
AlphaFold — — full sequence — Viewing
ColabFold KP13_02266
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 11.69 0.621
2 1.13 0.009

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.

56 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
6DB
5VVI
P0A4T4 246.3 Da LogP -1.23 TPSA 148.5 1 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O
AKG
5Y2V
P73862 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
OAS
4LQ2
P06614 147.1 Da LogP -1.04 TPSA 89.6 ✓ Ro5 ✓ Clean CC(=O)OC[C@@H](C(=O)O)N
RUB
5Z49
Q9F1R2 310.1 Da LogP -2.50 TPSA 191.0 1 viol. ✓ Clean C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O
SAC
4M4G
P06614 147.1 Da LogP -1.43 TPSA 86.6 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CO)C(=O)O
SKM
5TED
Q8Y9N7 174.2 Da LogP -1.52 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)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.