Protein profile

KP13_00948

Regulatory protein ada

Genome: KpKP13

Gene: ada AHE43524.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVL7
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Amino acids 354
Annotations 11
Features 39
PDB binders 2
Druggability 0.233

Overview

Basic information about this protein and its source genome.

Accession
KP13_00948
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ada AHE43524.1
Status
annotated
Amino acids
354
Structure source
AlphaFold + ColabFold
GO
GO:0008270 Binding to a zinc ion (Zn). GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. 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:0003908 Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.723
Human E-value
3.7e-15
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
81.02

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 0.233
Structure A0A0H3GVL7
Pocket Pocket 2
P2Rank 0.341
Structure A0A0H3GVL7
Pocket Pocket 1
ColabFold model
FPocket 0.703 · Pocket 18
P2Rank 0.122 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 93 / 4744 genomes with a hit
Normalized 0.02

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • 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:0003908 Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
  • 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.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006307 The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

39 records
Show feature table
Start End DB Term Name
1 76 Gene3D G3DSA:3.40.10.10 DNA Methylphosphotriester Repair Domain
1 76 InterPro IPR035451 Ada-like domain superfamily
99 181 SMART SM00342 aracneu4
99 181 InterPro IPR018060 DNA binding HTH domain, AraC-type
267 350 Gene3D G3DSA:1.10.10.10 -
267 350 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
80 146 Gene3D G3DSA:1.10.10.60 -
136 177 ProSitePatterns PS00041 Bacterial regulatory proteins, araC family signature.
136 177 InterPro IPR018062 HTH domain AraC-type, conserved site
189 266 SUPERFAMILY SSF53155 Methylated DNA-protein cysteine methyltransferase domain
189 266 InterPro IPR036631 Methylated DNA-protein cysteine methyltransferase domain superfamily
12 75 Pfam PF02805 Metal binding domain of Ada
12 75 InterPro IPR004026 Ada DNA repair, metal-binding
271 348 CDD cd06445 ATase
271 348 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
268 348 SUPERFAMILY SSF46767 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
268 348 InterPro IPR036217 Methylated DNA-protein cysteine methyltransferase, DNA binding domain
270 349 Pfam PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
270 349 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
319 325 ProSitePatterns PS00374 Methylated-DNA--protein-cysteine methyltransferase active site.
319 325 InterPro IPR001497 Methylated-DNA-[protein]-cysteine S-methyltransferase, active site
269 348 NCBIfam TIGR00589 methylated-DNA--[protein]-cysteine S-methyltransferase
269 348 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
190 248 Pfam PF02870 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
190 248 InterPro IPR008332 Methylguanine DNA methyltransferase, ribonuclease-like domain
3 92 SUPERFAMILY SSF57884 Ada DNA repair protein, N-terminal domain (N-Ada 10)
3 92 InterPro IPR035451 Ada-like domain superfamily
189 353 PANTHER PTHR10815 METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
85 183 ProSiteProfiles PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.
85 183 InterPro IPR018060 DNA binding HTH domain, AraC-type
1 354 PIRSF PIRSF000409 Ada
1 354 InterPro IPR016221 Bifunctional regulatory protein Ada
268 354 FunFam G3DSA:1.10.10.10:FF:000410 ADA regulatory protein, putative
85 133 SUPERFAMILY SSF46689 Homeodomain-like
85 133 InterPro IPR009057 Homeobox-like domain superfamily
105 182 Pfam PF12833 Helix-turn-helix domain
105 182 InterPro IPR018060 DNA binding HTH domain, AraC-type
175 266 Gene3D G3DSA:3.30.160.70 -
4 76 FunFam G3DSA:3.40.10.10:FF:000001 DNA-3-methyladenine glycosylase 2

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_A0A0H3GVL7
AlphaFold — — full sequence — Viewing
ColabFold KP13_00948
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 0.233

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 4.51 0.192
2 3.18 0.109
3 0.87 0.003
4 0.85 0.003
5 0.77 0.002

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.

5 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
ETW
6GA0
Q97VW7 479.5 Da LogP 5.21 TPSA 116.8 1 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C(=O)O)C3=C4C=CC(=…
OGQ
6Y8P
E5BBQ0 534.6 Da LogP 5.24 TPSA 85.8 2 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C3=C4C=CC(=[N+](C)…

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.