Protein profile

KP13_31565

UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

Genome: KpKP13

Gene: arnB AHE42233.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUE5
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Amino acids 379
Annotations 9
Features 18
PDB binders 4
Druggability 0.56

Overview

Basic information about this protein and its source genome.

Accession
KP13_31565
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
arnB AHE42233.1
Status
annotated
Amino acids
379
Structure source
AlphaFold + ColabFold
EC
2.6.1.87
GO
GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid. 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0099620 Catalysis of the reaction: UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo-pentopyranos-4-ulose + L-glutamate. 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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.14

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 0.56
Structure A0A0H3GUE5
Pocket Pocket 3
P2Rank 0.893
Structure A0A0H3GUE5
Pocket Pocket 1
ColabFold model
FPocket 0.665 · Pocket 13
P2Rank 0.842 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 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.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0099620 Catalysis of the reaction: UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo-pentopyranos-4-ulose + L-glutamate.
  • 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.

18 records
Show feature table
Start End DB Term Name
253 377 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
253 377 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
253 379 FunFam G3DSA:3.90.1150.10:FF:000030 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
4 376 SUPERFAMILY SSF53383 PLP-dependent transferases
4 376 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
1 252 FunFam G3DSA:3.40.640.10:FF:000040 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
12 374 Pfam PF01041 DegT/DnrJ/EryC1/StrS aminotransferase family
12 374 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
16 374 CDD cd00616 AHBA_syn
16 374 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
1 252 Gene3D G3DSA:3.40.640.10 -
1 252 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 379 PIRSF PIRSF000390 PLP_StrS
1 379 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
1 379 Hamap MF_01167 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase [arnB].
1 379 InterPro IPR022850 UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB
5 375 PANTHER PTHR30244 TRANSAMINASE
5 375 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase

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_A0A0H3GUE5
AlphaFold — — full sequence — Viewing
ColabFold KP13_31565
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
3 0.56
1 0.007
4 0.001
7 0.001

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 28.88 0.893
2 4.53 0.16
3 3.25 0.09
4 2.98 0.078
5 2.15 0.041

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.

22 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
AKG
1MDX
Q8ZNF3 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
DCS
1MDZ
Q8ZNF3 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
PGU
2OGA
Q9ZGH4 378.3 Da LogP 0.11 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)C(=O…
PMP
6EWR
A0A0H2URM1 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.