Protein profile

VK055_3626

putative 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD

Genome: KpATCC43816

Gene: AIK82181.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYK6
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Amino acids 300
Annotations 9
Features 10
PDB binders 0
Druggability 0.709

Overview

Basic information about this protein and its source genome.

Accession
VK055_3626
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82181.1
Status
annotated
Amino acids
300
Structure source
AlphaFold + ColabFold
EC
3.5.1.n3
GO
GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds. GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0036108 The chemical reactions and pathways resulting in the formation of 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate, a precursor of 4-amino-4-deoxy-L-arabinose (L-Ara4N). 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.

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 (%)
36.177
Localization
Cytoplasmic
ColabFold pLDDT
89.24

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 0.709
Structure A0A0H3GYK6
Pocket Pocket 2
P2Rank 0.591
Structure A0A0H3GYK6
Pocket Pocket 1
ColabFold model
FPocket 0.535 · Pocket 16
P2Rank 0.837 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 104 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
  • GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0036108 The chemical reactions and pathways resulting in the formation of 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate, a precursor of 4-amino-4-deoxy-L-arabinose (L-Ara4N).
  • 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:0046677 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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
2 268 PANTHER PTHR10587 GLYCOSYL TRANSFERASE-RELATED
1 295 Hamap MF_01870 Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD [arnD].
1 295 InterPro IPR023557 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD, probable
3 268 Gene3D G3DSA:3.20.20.370 Glycoside hydrolase/deacetylase
15 167 Pfam PF01522 Polysaccharide deacetylase
15 167 InterPro IPR002509 NodB homology domain
14 268 SUPERFAMILY SSF88713 Glycoside hydrolase/deacetylase
14 268 InterPro IPR011330 Glycoside hydrolase/deacetylase, beta/alpha-barrel
2 260 ProSiteProfiles PS51677 NodB homology domain profile.
2 260 InterPro IPR002509 NodB homology 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 + 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_A0A0H3GYK6
AlphaFold — — full sequence — Viewing
ColabFold VK055_3626
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 0.709

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 8.58 0.458