Protein profile

VK055_1381

23S rRNA pseudouridine synthase

Genome: KpATCC43816

Gene: AIK80004.1 yceC Structure source: AlphaFold + ColabFold UniProt A0A0H3GRG8
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Amino acids 317
Annotations 4
Features 23
PDB binders 1
Druggability 0.541

Overview

Basic information about this protein and its source genome.

Accession
VK055_1381
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80004.1 yceC
Status
annotated
Amino acids
317
Structure source
AlphaFold + ColabFold
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
38.961
Human E-value
1.38e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
93.103
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
89.84

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 0.541
Structure A0A0H3GRG8
Pocket Pocket 24
P2Rank 0.34
Structure A0A0H3GRG8
Pocket Pocket 1
ColabFold model
FPocket 0.133 · Pocket 4
P2Rank 0.329 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 197 / 4744 genomes with a hit
Normalized 0.042

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
16 314 NCBIfam TIGR00005 RluA family pseudouridine synthase
16 314 InterPro IPR006225 Pseudouridine synthase, RluC/RluD
20 79 SMART SM00363 s4_6
20 79 InterPro IPR002942 RNA-binding S4 domain
92 317 FunFam G3DSA:3.30.2350.10:FF:000007 Pseudouridine synthase
101 249 Pfam PF00849 RNA pseudouridylate synthase
101 249 InterPro IPR006145 Pseudouridine synthase, RsuA/RluA-like
102 287 CDD cd02869 PseudoU_synth_RluA_like
102 287 InterPro IPR006145 Pseudouridine synthase, RsuA/RluA-like
95 314 SUPERFAMILY SSF55120 Pseudouridine synthase
95 314 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
92 317 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase
20 83 ProSiteProfiles PS50889 S4 RNA-binding domain profile.
19 70 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif
20 66 Pfam PF01479 S4 domain
20 66 InterPro IPR002942 RNA-binding S4 domain
9 73 FunFam G3DSA:3.10.290.10:FF:000010 Pseudouridine synthase
20 106 CDD cd00165 S4
25 309 PANTHER PTHR21600 MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE
140 154 ProSitePatterns PS01129 Rlu family of pseudouridine synthase signature.
140 154 InterPro IPR006224 Pseudouridine synthase, RluA-like, conserved site
9 73 Gene3D G3DSA:3.10.290.10 -
9 73 InterPro IPR036986 RNA-binding S4 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_A0A0H3GRG8
AlphaFold — — full sequence — Viewing
ColabFold VK055_1381
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
23 0.223
1 0.021
25 0.002
20 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 7.67 0.34
2 3.81 0.119
3 3.45 0.099
4 1.12 0.008

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.