Protein profile

VK055_1471

glycyl-radical enzyme activating family protein

Genome: KpATCC43816

Gene: AIK80092.1 Structure source: AlphaFold + ColabFold UniProt A0A0C7KGK4
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Amino acids 291
Annotations 9
Features 25
PDB binders 1
Druggability 0.828

Overview

Basic information about this protein and its source genome.

Accession
VK055_1471
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80092.1
Status
annotated
Amino acids
291
Structure source
AlphaFold + ColabFold
EC
1.97.1.- 1.97.1.4
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: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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0043365 Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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 (%)
26.496
Localization
Cytoplasmic
ColabFold pLDDT
91.92

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 0.828
Structure A0A0C7KGK4
Pocket Pocket 14
P2Rank 0.955
Structure A0A0C7KGK4
Pocket Pocket 1
ColabFold model
FPocket 0.325 · Pocket 2
P2Rank 0.961 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 31 / 4744 genomes with a hit
Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 7 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

7
  • 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: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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0043365 Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
68 291 PIRSF PIRSF000371 PFLA_YjjW
68 291 InterPro IPR012839 Organic radical enzyme activase
14 81 PIRSF PIRSF000371 PFLA_YjjW
14 81 InterPro IPR012839 Organic radical enzyme activase
34 55 ProSitePatterns PS01087 Radical activating enzymes signature.
34 55 InterPro IPR001989 Radical-activating enzyme, conserved site
74 281 NCBIfam TIGR02494 glycyl-radical enzyme activating protein
32 282 ProSiteProfiles PS51918 Radical SAM core domain profile.
32 282 InterPro IPR007197 Radical SAM
19 284 PANTHER PTHR30352 PYRUVATE FORMATE-LYASE-ACTIVATING ENZYME
19 284 InterPro IPR034457 Organic radical-activating enzymes
21 92 SUPERFAMILY SSF54862 4Fe-4S ferredoxins
73 257 SUPERFAMILY SSF102114 Radical SAM enzymes
33 156 Pfam PF13353 4Fe-4S single cluster domain
40 246 CDD cd01335 Radical_SAM
18 290 SFLD SFLDG01118 activating enzymes, group 2
18 290 InterPro IPR040074 BssD/PflA/YjjW
40 221 Pfam PF04055 Radical SAM superfamily
40 221 InterPro IPR007197 Radical SAM
18 290 SFLD SFLDS00029 Radical SAM
18 290 InterPro IPR007197 Radical SAM
20 289 Gene3D G3DSA:3.20.20.70 Aldolase class I
20 289 InterPro IPR013785 Aldolase-type TIM barrel
63 95 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
63 95 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain

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_A0A0C7KGK4
AlphaFold — — full sequence — Viewing
ColabFold VK055_1471
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
14 0.828

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 27.95 0.923
2 1.41 0.018

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

1 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
MT2
3C8F
P0A9N4 178.3 Da LogP 0.06 TPSA 63.3 ✓ Ro5 ✓ Clean CC[S@@+](C)CC[C@@H](C(=O)O)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.