Protein profile

VK055_4409

tRNA pseudouridine 13 synthase

Genome: KpATCC43816

Gene: AIK82952.1 ygbO Structure source: AlphaFold + ColabFold UniProt A0A0H3GSA7
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Amino acids 349
Annotations 8
Features 22
PDB binders 0
Druggability 0.545

Overview

Basic information about this protein and its source genome.

Accession
VK055_4409
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82952.1 ygbO
Status
annotated
Amino acids
349
Structure source
AlphaFold + ColabFold
EC
5.4.99.27
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0160150 Catalysis of the reaction: uridine(13) in tRNA = pseudouridine(13) in tRNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.479
Human E-value
1.39e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
44.38
DEG E-value
4.26e-85
Localization
Cytoplasmic
ColabFold pLDDT
94.96

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 0.545
Structure A0A0H3GSA7
Pocket Pocket 17
P2Rank 0.9
Structure A0A0H3GSA7
Pocket Pocket 1
ColabFold model
FPocket 0.655 · Pocket 1
P2Rank 0.597 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 109 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0160150 Catalysis of the reaction: uridine(13) in tRNA = pseudouridine(13) in tRNA.
  • GO:0031119 The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
1 340 PANTHER PTHR47811 TRNA PSEUDOURIDINE SYNTHASE D
167 301 FunFam G3DSA:3.30.2340.10:FF:000001 tRNA pseudouridine synthase D
18 338 CDD cd02575 PseudoU_synth_EcTruD
16 202 FunFam G3DSA:3.30.2350.20:FF:000001 tRNA pseudouridine synthase D
77 90 ProSitePatterns PS01268 Uncharacterized protein family UPF0024 signature.
77 90 InterPro IPR020119 Pseudouridine synthase TruD, conserved site
155 303 ProSiteProfiles PS50984 TRUD domain profile.
155 303 InterPro IPR011760 Pseudouridine synthase, TruD, insertion domain
1 342 NCBIfam TIGR00094 tRNA pseudouridine(13) synthase TruD
1 342 InterPro IPR001656 Pseudouridine synthase, TruD
17 337 Gene3D G3DSA:3.30.2350.20 TruD, catalytic domain
17 337 InterPro IPR042214 Pseudouridine synthase, TruD, catalytic domain
10 167 Pfam PF01142 tRNA pseudouridine synthase D (TruD)
10 167 InterPro IPR001656 Pseudouridine synthase, TruD
188 337 Pfam PF01142 tRNA pseudouridine synthase D (TruD)
188 337 InterPro IPR001656 Pseudouridine synthase, TruD
3 340 SUPERFAMILY SSF55120 Pseudouridine synthase
3 340 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
5 342 Hamap MF_01082 tRNA pseudouridine synthase D [truD].
5 342 InterPro IPR001656 Pseudouridine synthase, TruD
167 301 Gene3D G3DSA:3.30.2340.10 TruD, insertion domain
167 301 InterPro IPR043165 Pseudouridine synthase, TruD, insertion 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_A0A0H3GSA7
AlphaFold — — full sequence — Viewing
ColabFold VK055_4409
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
17 0.545
2 0.245
18 0.007
21 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 29.96 0.9
2 8.99 0.413
3 4.87 0.18
4 1.1 0.007