Protein profile

VK055_3627

4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

Genome: KpATCC43816

Gene: arnT AIK82182.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZQ8
Amino acids 551
Annotations 10
Features 41
PDB binders 4
Druggability 0.915

Overview

Basic information about this protein and its source genome.

Accession
VK055_3627
Gene
arnT AIK82182.1
Status
annotated
Amino acids
551
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
62.795
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
92.78

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 0.915
Structure A0A0H3GZQ8
Pocket Pocket 1
P2Rank 0.933
Structure A0A0H3GZQ8
Pocket Pocket 1
ColabFold model
FPocket 0.925 · Pocket 2
P2Rank 0.904 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 73 / 4744 genomes with a hit
Normalized 0.015

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0000030 Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
  • GO:0006493 A glycoprotein biosynthetic process starting with the covalent linkage of carbohydrate or carbohydrate derivative unit via a glycosidic bond to the oxygen atom of a serine, threonine, hydroxylysine, hydroxyproline or tyrosine side chain in a protein, which can be further elongated with the sequential addition of sugar units resulting in the formation of a protein O-linked glycan.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0103015 Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate.
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • GO:0010041 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(III) ion stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
112 134 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
132 137 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
334 344 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
112 131 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
310 314 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
207 227 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
10 542 PANTHER PTHR33908 MANNOSYLTRANSFERASE YKCB-RELATED
1 551 Hamap MF_01165 Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase [arnT].
1 551 InterPro IPR022839 Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
384 401 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
408 426 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
315 333 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
280 290 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
291 309 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
175 197 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
157 161 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
162 195 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
402 407 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
384 401 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
292 309 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
138 156 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
204 226 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
107 111 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
81 103 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
347 369 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
365 383 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 237 Pfam PF02366 Dolichyl-phosphate-mannose-protein mannosyltransferase
4 237 InterPro IPR003342 Glycosyl transferase family 39/83
345 364 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
228 256 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
427 551 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
408 427 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
85 106 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 84 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
196 206 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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_A0A0H3GZQ8
AlphaFold full sequence Viewing
ColabFold VK055_3627
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
1 0.915
4 0.854

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 19.07 0.834
2 14.19 0.714
3 6.78 0.347
4 4.64 0.202
5 4.49 0.191

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.

55 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
5TR Q1LDT6 847.3 Da LogP 18.33 TPSA 66.8 2 viol. ✓ Clean CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC…
DSL Q1LDT6 779.2 Da LogP 16.60 TPSA 66.8 2 viol. ✓ Clean CC(=CCC/C(=C/CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC…
MPG Q1LDT6 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O
PC Q1LDT6 184.2 Da LogP -0.20 TPSA 66.8 ✓ Ro5 ✓ Clean C[N+](C)(C)CCOP(=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.