Protein profile

VK055_4089

radical SAM superfamily protein

Genome: KpATCC43816

Gene: AIK82635.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXJ4
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Amino acids 379
Annotations 7
Features 23
PDB binders 0
Druggability 0.781

Overview

Basic information about this protein and its source genome.

Accession
VK055_4089
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82635.1
Status
annotated
Amino acids
379
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:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX. 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:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.42
Human E-value
1.65e-18
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
35.398
Localization
Cytoplasmic
ColabFold pLDDT
96.02

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 0.781
Structure A0A0H3GXJ4
Pocket Pocket 2
P2Rank 0.986
Structure A0A0H3GXJ4
Pocket Pocket 1
ColabFold model
FPocket 0.207 · Pocket 2
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 163 / 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.

7 GO

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:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX.
  • 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:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
304 364 Pfam PF06969 HemN C-terminal domain
304 364 InterPro IPR010723 HemN, C-terminal
5 376 SUPERFAMILY SSF102114 Radical SAM enzymes
7 368 NCBIfam TIGR00539 radical SAM family heme chaperone HemW
7 368 InterPro IPR004559 Heme chaperone HemW-like
9 218 Gene3D G3DSA:3.20.20.70 Aldolase class I
9 218 InterPro IPR013785 Aldolase-type TIM barrel
2 376 SFLD SFLDS00029 Radical SAM
2 376 InterPro IPR007197 Radical SAM
15 216 CDD cd01335 Radical_SAM
1 234 ProSiteProfiles PS51918 Radical SAM core domain profile.
1 234 InterPro IPR007197 Radical SAM
2 376 SFLD SFLDF00288 HemN-like, clustered with nucleoside-triphosphate RdgB
6 377 PANTHER PTHR13932 COPROPORPHYRINIGEN III OXIDASE
6 377 InterPro IPR034505 Anaerobic coproporphyrinogen-III oxidase
6 376 SFLD SFLDF00562 HemN-like, clustered with heat shock genes
6 376 InterPro IPR004559 Heme chaperone HemW-like
6 223 SMART SM00729 MiaB
6 223 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
11 179 Pfam PF04055 Radical SAM superfamily
11 179 InterPro IPR007197 Radical SAM
9 222 FunFam G3DSA:3.20.20.70:FF:000124 Heme chaperone HemW
16 241 SFLD SFLDG01082 B12-binding domain containing

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_A0A0H3GXJ4
AlphaFold — — full sequence — Viewing
ColabFold VK055_4089
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 0.781
1 0.494

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 46.69 0.975
2 1.82 0.035
3 0.95 0.005