Protein profile

KP13_04279

Ribosomal protein S12 methylthiotransferase RimO

Genome: KpKP13

Gene: rimO AHE45513.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLY2
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Amino acids 441
Annotations 8
Features 40
PDB binders 2
Druggability 0.499

Overview

Basic information about this protein and its source genome.

Accession
KP13_04279
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rimO AHE45513.1
Status
annotated
Amino acids
441
Structure source
AlphaFold + ColabFold
GO
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0035596 Catalysis of the addition of a methylthioether group (-SCH3) to a nucleic acid or protein acceptor. GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.677
Human E-value
2.28e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.558
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
93.65

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 0.499
Structure A0A0H3GLY2
Pocket Pocket 2
P2Rank 0.913
Structure A0A0H3GLY2
Pocket Pocket 1
ColabFold model
FPocket 0.759 · Pocket 26
P2Rank 0.924 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 234 / 4744 genomes with a hit
Normalized 0.049

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0035596 Catalysis of the addition of a methylthioether group (-SCH3) to a nucleic acid or protein acceptor.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • 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:0018339 The modification of peptidyl-aspartic acid to form peptidyl-L-beta-methylthioaspartic acid, typical of bacterial ribosomal protein S12.

Sequence Features

Domain/signature hits from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
106 371 SUPERFAMILY SSF102114 Radical SAM enzymes
53 362 SFLD SFLDG01082 B12-binding domain containing
138 379 FunFam G3DSA:3.80.30.20:FF:000001 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2
146 323 Pfam PF04055 Radical SAM superfamily
146 323 InterPro IPR007197 Radical SAM
140 365 SMART SM00729 MiaB
140 365 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
380 441 Gene3D G3DSA:2.40.50.140 -
380 441 InterPro IPR012340 Nucleic acid-binding, OB-fold
5 439 SFLD SFLDF00274 ribosomal protein S12 methylthiotransferase (RimO-like)
5 439 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
9 438 NCBIfam TIGR01125 30S ribosomal protein S12 methylthiotransferase RimO
9 438 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
5 440 PANTHER PTHR43837 RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO
5 440 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
379 441 Pfam PF18693 TRAM domain
379 441 InterPro IPR041582 RimO, TRAM domain
136 373 ProSiteProfiles PS51918 Radical SAM core domain profile.
136 373 InterPro IPR007197 Radical SAM
5 439 SFLD SFLDG01061 methylthiotransferase
5 439 InterPro IPR005839 Methylthiotransferase
138 379 Gene3D G3DSA:3.80.30.20 tm_1862 like domain
138 379 InterPro IPR023404 Radical SAM, alpha/beta horseshoe
9 125 FunFam G3DSA:3.40.50.12160:FF:000002 Ribosomal protein S12 methylthiotransferase RimO
144 164 ProSitePatterns PS01278 Methylthiotransferase radical SAM domain signature.
144 164 InterPro IPR020612 Methylthiotransferase, conserved site
8 118 ProSiteProfiles PS51449 Methylthiotransferase N-terminal domain profile.
8 118 InterPro IPR013848 Methylthiotransferase, N-terminal
9 438 NCBIfam TIGR00089 MiaB/RimO family radical SAM methylthiotransferase
9 438 InterPro IPR005839 Methylthiotransferase
9 95 Pfam PF00919 Uncharacterized protein family UPF0004
9 95 InterPro IPR013848 Methylthiotransferase, N-terminal
9 126 Gene3D G3DSA:3.40.50.12160 -
9 126 InterPro IPR038135 Methylthiotransferase, N-terminal domain superfamily
376 441 ProSiteProfiles PS50926 TRAM domain profile.
376 441 InterPro IPR002792 TRAM domain
144 354 CDD cd01335 Radical_SAM
8 440 Hamap MF_01865 Ribosomal protein S12 methylthiotransferase RimO [rimO].
8 440 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
380 441 FunFam G3DSA:2.40.50.140:FF:000060 Ribosomal protein S12 methylthiotransferase RimO

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_A0A0H3GLY2
AlphaFold — — full sequence — Viewing
ColabFold KP13_04279
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 0.499
28 0.033
6 0.011
10 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 31.91 0.913
2 7.77 0.347
3 6.83 0.294
4 2.59 0.06
5 1.1 0.007

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.

15 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
CXS
2QGQ
Q9X2H6 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
FS5
4JC0
Q9X2H6 863.6 Da LogP 8.41 TPSA 0.0 2 viol. ✓ Clean S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[F…

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.