Protein profile

VK055_2920

kamA family protein

Genome: KpATCC43816

Gene: AIK81506.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQG9
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Amino acids 320
Annotations 5
Features 21
PDB binders 0
Druggability 0.955

Overview

Basic information about this protein and its source genome.

Accession
VK055_2920
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81506.1
Status
annotated
Amino acids
320
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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. 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:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. 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)
Y
DEG identity (%)
59.615
DEG E-value
7.78e-142
Localization
Cytoplasmic
ColabFold pLDDT
96.78

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 0.955
Structure A0A0H3GQG9
Pocket Pocket 1
P2Rank 0.979
Structure A0A0H3GQG9
Pocket Pocket 1
ColabFold model
FPocket 0.96 · Pocket 5
P2Rank 0.982 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • 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:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
92 289 CDD cd01335 Radical_SAM
2 313 PANTHER PTHR30538 LYSINE 2,3-AMINOMUTASE-RELATED
2 313 InterPro IPR003739 Lysine-2,3-aminomutase/glutamate 2,3-aminomutase
96 241 Pfam PF04055 Radical SAM superfamily
96 241 InterPro IPR007197 Radical SAM
2 314 SFLD SFLDG01070 PLP-dependent
2 314 InterPro IPR003739 Lysine-2,3-aminomutase/glutamate 2,3-aminomutase
1 320 PIRSF PIRSF004911 L-lysine_2_3-aminomutase
1 320 InterPro IPR003739 Lysine-2,3-aminomutase/glutamate 2,3-aminomutase
90 155 Pfam PF13353 4Fe-4S single cluster domain
80 302 SUPERFAMILY SSF102114 Radical SAM enzymes
2 313 NCBIfam TIGR03821 EF-P beta-lysylation protein EpmB
2 313 InterPro IPR022462 Lysine-2,3-aminomutase-like
2 314 SFLD SFLDF00314 L-lysine 2,3-aminomutase (yjeK like)
2 314 InterPro IPR022462 Lysine-2,3-aminomutase-like
84 307 ProSiteProfiles PS51918 Radical SAM core domain profile.
84 307 InterPro IPR007197 Radical SAM
29 312 Gene3D G3DSA:3.20.20.70 Aldolase class I
29 312 InterPro IPR013785 Aldolase-type TIM barrel
2 306 NCBIfam TIGR00238 KamA family radical SAM protein
2 306 InterPro IPR003739 Lysine-2,3-aminomutase/glutamate 2,3-aminomutase

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_A0A0H3GQG9
AlphaFold — — full sequence — Viewing
ColabFold VK055_2920
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 0.955
4 0.245

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 40.36 0.964
2 1.64 0.027