Protein profile

VK055_4858

NUDIX domain protein

Genome: KpATCC43816

Gene: AIK83385.1 Structure source: Experimental + ColabFold UniProt A0A1W1Q5B1
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Amino acids 141
Annotations 9
Features 16
PDB binders 0
Druggability 0.472

Overview

Basic information about this protein and its source genome.

Accession
VK055_4858
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83385.1
Status
annotated
Amino acids
141
Structure source
Experimental + ColabFold
EC
3.6.1.9 3.6.1.12 3.6.1.- 3.6.1.23
GO
GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0047840 Catalysis of the reaction: dCTP + H2O = dCMP + H+ + diphosphate. GO:0004170 Catalysis of the reaction: dUTP + H2O = dUMP + H+ + diphosphate. GO:0000287 Binding to a magnesium (Mg) ion.

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 (%)
28.571
Localization
Cytoplasmic
ColabFold pLDDT
95.43

Selected Druggability evidence

PDB experimental structure

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 0.472
Structure 6DT3
Pocket Pocket 1
P2Rank 0.717
Structure 6DT3
Pocket Pocket 1
ColabFold model
FPocket 0.319 · Pocket 7
P2Rank 0.602 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 50 / 4744 genomes with a hit
Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 EC 5 GO

Enzyme Commission (EC)

4

Gene Ontology (GO)

5
  • GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0047840 Catalysis of the reaction: dCTP + H2O = dCMP + H+ + diphosphate.
  • GO:0004170 Catalysis of the reaction: dUTP + H2O = dUMP + H+ + diphosphate.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 141 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
1 141 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
1 141 InterPro IPR000086 NUDIX hydrolase domain
1 129 Pfam PF00293 NUDIX domain
1 129 InterPro IPR000086 NUDIX hydrolase domain
10 126 PANTHER PTHR43046 GDP-MANNOSE MANNOSYL HYDROLASE
47 62 PRINTS PR00502 NUDIX hydrolase family signature
47 62 InterPro IPR020476 NUDIX hydrolase
33 47 PRINTS PR00502 NUDIX hydrolase family signature
33 47 InterPro IPR020476 NUDIX hydrolase
38 59 ProSitePatterns PS00893 Nudix box signature.
38 59 InterPro IPR020084 NUDIX hydrolase, conserved site
2 127 SUPERFAMILY SSF55811 Nudix
2 127 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
1 141 Hamap MF_01846 Nucleoside triphosphatase NudI [nudI].
1 141 InterPro IPR023781 Nucleoside triphosphatase NudI

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6DT3
X-ray 1.20 Å A,B
100.0% 1-141
PDBe RCSB PDBj File
Viewing
ColabFold VK055_4858
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
1 0.858

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 32.63 0.944
2 14.17 0.714
3 4.47 0.19
4 1.48 0.021