Protein profile

VK055_2071

tRNA 2-selenouridine synthase

Genome: KpATCC43816

Gene: AIK80676.1 selU Structure source: AlphaFold + ColabFold UniProt A0A0H3GKN1
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Amino acids 358
Annotations 4
Features 16
PDB binders 0
Druggability 0.346

Overview

Basic information about this protein and its source genome.

Accession
VK055_2071
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80676.1 selU
Status
annotated
Amino acids
358
Structure source
AlphaFold + ColabFold
EC
2.9.1.3
GO
GO:0043828 Catalysis of the reaction: 5-methylaminomethyl-2-thiouridine + selenophosphate = 5-methylaminomethyl-2-selenouridine + phosphate (at the wobble position in tRNA). GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon. GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).

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
96.33

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 0.346
Structure A0A0H3GKN1
Pocket Pocket 16
P2Rank 0.852
Structure A0A0H3GKN1
Pocket Pocket 1
ColabFold model
FPocket 0.842 · Pocket 1
P2Rank 0.915 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 83 / 4744 genomes with a hit
Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0043828 Catalysis of the reaction: 5-methylaminomethyl-2-thiouridine + selenophosphate = 5-methylaminomethyl-2-selenouridine + phosphate (at the wobble position in tRNA).
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 358 Hamap MF_01622 tRNA 2-selenouridine synthase [selU].
1 358 InterPro IPR017582 tRNA 2-selenouridine synthase
7 131 Gene3D G3DSA:3.40.250.10 -
7 131 InterPro IPR036873 Rhodanese-like domain superfamily
3 357 PANTHER PTHR30401 TRNA 2-SELENOURIDINE SYNTHASE
3 357 InterPro IPR017582 tRNA 2-selenouridine synthase
1 131 SMART SM00450 rhod_4
1 131 InterPro IPR001763 Rhodanese-like domain
6 153 SUPERFAMILY SSF52821 Rhodanese/Cell cycle control phosphatase
6 153 InterPro IPR036873 Rhodanese-like domain superfamily
2 131 FunFam G3DSA:3.40.250.10:FF:000009 tRNA 2-selenouridine/geranyl-2-thiouridine synthase
11 134 ProSiteProfiles PS50206 Rhodanese domain profile.
11 134 InterPro IPR001763 Rhodanese-like domain
5 129 CDD cd01520 RHOD_YbbB
14 342 NCBIfam TIGR03167 tRNA 2-selenouridine(34) synthase MnmH
14 342 InterPro IPR017582 tRNA 2-selenouridine 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_A0A0H3GKN1
AlphaFold — — full sequence — Viewing
ColabFold VK055_2071
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
16 0.346
1 0.004
11 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 24.29 0.852
2 8.06 0.362
3 5.94 0.241
4 5.71 0.229
5 1.83 0.029