Protein profile

VK055_3806

tRNA dihydrouridine synthase

Genome: KpATCC43816

Gene: yhdG AIK82356.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H3Q9
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Amino acids 290
Annotations 4
Features 18
PDB binders 0
Druggability 0.382

Overview

Basic information about this protein and its source genome.

Accession
VK055_3806
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
yhdG AIK82356.1
Status
annotated
Amino acids
290
Structure source
AlphaFold + ColabFold
GO
GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GO:0017150 Catalysis of the reaction: a 5,6-dihydrouridine in tRNA + NAD(P)+ = a uridine in tRNA + H+ + NAD(P)H. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.5
Human E-value
1.54e-13
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
30.256
Localization
Cytoplasmic
ColabFold pLDDT
92.95

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 0.382
Structure A0A0H3H3Q9
Pocket Pocket 4
P2Rank 0.535
Structure A0A0H3H3Q9
Pocket Pocket 1
ColabFold model
FPocket 0.398 · Pocket 8
P2Rank 0.59 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 199 / 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:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0017150 Catalysis of the reaction: a 5,6-dihydrouridine in tRNA + NAD(P)+ = a uridine in tRNA + H+ + NAD(P)H.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
221 290 Gene3D G3DSA:1.10.1200.80 Putative flavin oxidoreducatase; domain 2
221 290 InterPro IPR024036 tRNA-dihydrouridine synthase, putative, C-terminal
1 289 NCBIfam TIGR00737 tRNA dihydrouridine synthase DusB
1 289 InterPro IPR004652 tRNA-dihydrouridine synthase DusB-like
1 211 CDD cd02801 DUS_like_FMN
1 211 InterPro IPR035587 DUS-like, FMN-binding domain
1 290 PIRSF PIRSF006621 Dus
1 290 InterPro IPR001269 tRNA-dihydrouridine synthase
1 210 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 210 InterPro IPR013785 Aldolase-type TIM barrel
2 258 PANTHER PTHR45846 TRNA-DIHYDROURIDINE(47) SYNTHASE [NAD(P)(+)]-LIKE
2 287 Pfam PF01207 Dihydrouridine synthase (Dus)
2 287 InterPro IPR035587 DUS-like, FMN-binding domain
221 290 FunFam G3DSA:1.10.1200.80:FF:000001 tRNA-dihydrouridine synthase B
1 216 FunFam G3DSA:3.20.20.70:FF:000051 tRNA-dihydrouridine synthase B
63 81 ProSitePatterns PS01136 Uncharacterized protein family UPF0034 signature.
63 81 InterPro IPR018517 tRNA-dihydrouridine synthase, conserved site
2 288 SUPERFAMILY SSF51395 FMN-linked oxidoreductases

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_A0A0H3H3Q9
AlphaFold — — full sequence — Viewing
ColabFold VK055_3806
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
7 0.252
5 0.251
9 0.149
10 0.047

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 11.62 0.535
2 6.89 0.297
3 6.2 0.257
4 2.01 0.036
5 1.64 0.022