Protein profile

KP13_00326

Bifunctional polymyxin resistance protein ArnA

Genome: KpKP13

Gene: AHE42234.1 arnA Structure source: AlphaFold + ColabFold UniProt A0A0H3GX03
Export view
Amino acids 661
Annotations 10
Features 23
PDB binders 5
Druggability 0.853

Overview

Basic information about this protein and its source genome.

Accession
KP13_00326
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42234.1 arnA
Status
annotated
Amino acids
661
Structure source
AlphaFold + ColabFold
GO
GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound. GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. 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:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl 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:0099619 Catalysis of the reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.462
Human E-value
5.84e-09
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.04

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 0.853
Structure A0A0H3GX03
Pocket Pocket 4
P2Rank 0.964
Structure A0A0H3GX03
Pocket Pocket 1
ColabFold model
FPocket 0.226 · Pocket 5
P2Rank 0.954 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 115 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • 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:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl 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:0099619 Catalysis of the reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose.
  • GO:0099618 Catalysis of the reaction: UDP-alpha-D-glucuronate + NAD+ = UDP-beta-L-threo-pentopyranos-4-ulose + CO2 + NADH.
  • 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.

23 records
Show feature table
Start End DB Term Name
1 303 Gene3D G3DSA:3.40.50.12230 -
1 202 SUPERFAMILY SSF53328 Formyltransferase
1 202 InterPro IPR036477 Formyl transferase, N-terminal domain superfamily
314 660 FunFam G3DSA:3.40.50.720:FF:000197 Bifunctional polymyxin resistance protein ArnA
318 566 Pfam PF01370 NAD dependent epimerase/dehydratase family
318 566 InterPro IPR001509 NAD-dependent epimerase/dehydratase
202 294 Pfam PF02911 Formyl transferase, C-terminal domain
202 294 InterPro IPR005793 Formyl transferase, C-terminal
204 292 CDD cd08702 Arna_FMT_C
26 177 Pfam PF00551 Formyl transferase
26 177 InterPro IPR002376 Formyl transferase, N-terminal
316 652 PANTHER PTHR43245 BIFUNCTIONAL POLYMYXIN RESISTANCE PROTEIN ARNA
1 203 CDD cd08644 FMT_core_ArnA_N
1 660 Hamap MF_01166 Bifunctional polymyxin resistance protein ArnA [arnA].
1 660 InterPro IPR021168 Bifunctional polymyxin resistance protein, ArnA
314 660 Gene3D G3DSA:3.40.50.720 -
204 302 SUPERFAMILY SSF50486 FMT C-terminal domain-like
204 302 InterPro IPR011034 Formyl transferase-like, C-terminal domain superfamily
317 652 CDD cd05257 Arna_like_SDR_e
317 652 InterPro IPR045869 Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs
1 660 PIRSF PIRSF036506 MtRNA_frt_NDPSE
317 652 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
317 652 InterPro IPR036291 NAD(P)-binding domain superfamily

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_A0A0H3GX03
AlphaFold — — full sequence — Viewing
ColabFold KP13_00326
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
4 0.853
24 0.252

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 26.25 0.912
2 18.12 0.815
3 5.14 0.236
4 3.05 0.101

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
DTT
4WKG
P77398 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FME
2FMT
P23882 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
MOE
3R8X
Q8ZJ80 75.1 Da LogP -1.01 TPSA 32.3 ✓ Ro5 ✓ Clean COCC[O-]
PG5
4IQF
Q81WH2 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
UGA
1Z7E
P77398 580.3 Da LogP -4.70 TPSA 314.1 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)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.