Protein profile

VK055_0178

RNA pseudouridylate synthase family protein

Genome: KpATCC43816

Gene: AIK78806.1 Structure source: AlphaFold + ColabFold UniProt A0A377WKT2
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Amino acids 232
Annotations 7
Features 10
PDB binders 1
Druggability 0.598

Overview

Basic information about this protein and its source genome.

Accession
VK055_0178
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78806.1
Status
annotated
Amino acids
232
Structure source
AlphaFold + ColabFold
EC
5.4.99.28
GO
GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5. GO:0160151 Catalysis of the reaction: uridine(32) in tRNA = pseudouridine(32) in tRNA. GO:0000455 The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
45.946
Human E-value
8.98e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
40.09
DEG E-value
7.590000000000001e-47
Localization
Cytoplasmic
ColabFold pLDDT
96.16

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 0.598
Structure A0A377WKT2
Pocket Pocket 18
P2Rank 0.607
Structure A0A377WKT2
Pocket Pocket 1
ColabFold model
FPocket 0.759 · Pocket 7
P2Rank 0.524 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 86 / 4744 genomes with a hit
Normalized 0.018

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
  • GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
  • GO:0160151 Catalysis of the reaction: uridine(32) in tRNA = pseudouridine(32) in tRNA.
  • GO:0000455 The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
25 180 Pfam PF00849 RNA pseudouridylate synthase
25 180 InterPro IPR006145 Pseudouridine synthase, RsuA/RluA-like
26 215 CDD cd02869 PseudoU_synth_RluA_like
26 215 InterPro IPR006145 Pseudouridine synthase, RsuA/RluA-like
63 77 ProSitePatterns PS01129 Rlu family of pseudouridine synthase signature.
63 77 InterPro IPR006224 Pseudouridine synthase, RluA-like, conserved site
18 231 SUPERFAMILY SSF55120 Pseudouridine synthase
18 231 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
8 230 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase
18 220 PANTHER PTHR21600 MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE

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_A0A377WKT2
AlphaFold — — full sequence — Viewing
ColabFold VK055_0178
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
18 0.598
19 0.003
1 0.002
3 0.0

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 13.57 0.607
2 8.62 0.393

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.

1 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
FOU
2I82
P0AA37 150.1 Da LogP -1.73 TPSA 81.6 ✓ Ro5 ✓ Clean [C@H]1(C([C@H](NC(=O)N1)O)F)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.