Protein profile

VK055_1810

conserved metal-binding protein

Genome: KpATCC43816

Gene: AIK80423.1 ybgI Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ01
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Amino acids 247
Annotations 3
Features 12
PDB binders 0
Druggability 0.495

Overview

Basic information about this protein and its source genome.

Accession
VK055_1810
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80423.1 ybgI
Status
annotated
Amino acids
247
Structure source
AlphaFold + ColabFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0046872 Binding to a metal 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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
98.43

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 0.495
Structure A0A0H3GQ01
Pocket Pocket 7
P2Rank 0.868
Structure A0A0H3GQ01
Pocket Pocket 1
ColabFold model
FPocket 0.451 · Pocket 6
P2Rank 0.892 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
7 235 Gene3D G3DSA:3.40.1390.30 -
100 218 FunFam G3DSA:3.40.1390.30:FF:000002 Nif3-like dinuclear metal center protein
97 218 Gene3D G3DSA:3.40.1390.30 -
7 99 FunFam G3DSA:3.40.1390.30:FF:000003 Nif3-like dinuclear metal center protein
1 246 SUPERFAMILY SSF102705 NIF3 (NGG1p interacting factor 3)-like
1 246 InterPro IPR036069 DUF34/NIF3 superfamily
7 234 Pfam PF01784 NIF3 (NGG1p interacting factor 3)
7 234 InterPro IPR002678 DUF34/NIF3
1 246 NCBIfam TIGR00486 Nif3-like dinuclear metal center hexameric protein
1 246 InterPro IPR002678 DUF34/NIF3
1 239 PANTHER PTHR13799 NGG1 INTERACTING FACTOR 3
1 239 InterPro IPR002678 DUF34/NIF3

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

Loading 3D structure...

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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_A0A0H3GQ01
AlphaFold — — full sequence — Viewing
ColabFold VK055_1810
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
2 0.216
4 0.005
1 0.003
9 0.002

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 25.78 0.868
2 1.4 0.015
3 1.32 0.012