Protein profile

VK055_4040

radical SAM superfamily protein

Genome: KpATCC43816

Gene: AIK82587.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H356
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Amino acids 727
Annotations 3
Features 27
PDB binders 0
Druggability 0.546

Overview

Basic information about this protein and its source genome.

Accession
VK055_4040
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82587.1
Status
annotated
Amino acids
727
Structure source
AlphaFold + ColabFold
GO
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

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
88.34

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 0.546
Structure A0A0H3H356
Pocket Pocket 5
P2Rank 0.961
Structure A0A0H3H356
Pocket Pocket 1
ColabFold model
FPocket 0.723 · Pocket 3
P2Rank 0.965 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 127 / 4744 genomes with a hit
Normalized 0.027

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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
14 692 PANTHER PTHR32331 UPF0313 PROTEIN YGIQ
14 692 InterPro IPR022946 Uncharacterised protein family UPF0313
15 700 SFLD SFLDS00029 Radical SAM
15 700 InterPro IPR007197 Radical SAM
29 646 Hamap MF_01251 UPF0313 protein YgiQ [ygiQ].
29 646 InterPro IPR022946 Uncharacterised protein family UPF0313
688 727 MobiDBLite mobidb-lite consensus disorder prediction
376 626 SMART SM00729 MiaB
376 626 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
29 379 Pfam PF08497 Radical SAM N-terminal
29 379 InterPro IPR013704 UPF0313, N-terminal
15 700 SFLD SFLDG01069 UPF0313
15 700 InterPro IPR022946 Uncharacterised protein family UPF0313
46 604 SFLD SFLDG01082 B12-binding domain containing
380 585 Pfam PF04055 Radical SAM superfamily
380 585 InterPro IPR007197 Radical SAM
371 647 SUPERFAMILY SSF102114 Radical SAM enzymes
372 650 ProSiteProfiles PS51918 Radical SAM core domain profile.
372 650 InterPro IPR007197 Radical SAM
594 713 Pfam PF11842 Domain of unknown function (DUF3362)
594 713 InterPro IPR024560 UPF0313, C-terminal
380 400 ProSitePatterns PS01278 Methylthiotransferase radical SAM domain signature.
380 400 InterPro IPR020612 Methylthiotransferase, conserved site
375 620 Gene3D G3DSA:3.80.30.20 tm_1862 like domain
375 620 InterPro IPR023404 Radical SAM, alpha/beta horseshoe
29 644 NCBIfam TIGR03904 YgiQ family radical SAM protein
29 644 InterPro IPR022946 Uncharacterised protein family UPF0313

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_A0A0H3H356
AlphaFold — — full sequence — Viewing
ColabFold VK055_4040
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
5 0.546
31 0.017
51 0.001
12 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 46.61 0.961
2 10.42 0.482
3 7.17 0.312
4 5.53 0.218
5 3.11 0.084