Protein profile

VK055_4569

16S rRNA processing protein RimM

Genome: KpATCC43816

Gene: AIK83107.1 rimM Structure source: AlphaFold + ColabFold UniProt A0A0H3H1R7
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Amino acids 152
Annotations 5
Features 17
PDB binders 0
Druggability 0.016

Overview

Basic information about this protein and its source genome.

Accession
VK055_4569
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83107.1 rimM
Status
annotated
Amino acids
152
Structure source
AlphaFold + ColabFold
GO
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0043022 Binding to a ribosome. GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0042274 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.

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 (%)
92.763
DEG E-value
1.53e-105
Localization
Cytoplasmic
ColabFold pLDDT
85.73

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 0.016
Structure A0A0H3H1R7
Pocket Pocket 7
P2Rank 0.078
Structure A0A0H3H1R7
Pocket Pocket 1
ColabFold model
FPocket 0.005 · Pocket 10
P2Rank 0.088 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 132 / 4744 genomes with a hit
Normalized 0.028

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:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0043022 Binding to a ribosome.
  • GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0042274 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
2 152 Hamap MF_00014 Ribosome maturation factor RimM [rimM].
2 152 InterPro IPR011961 16S rRNA processing protein RimM
71 152 FunFam G3DSA:2.30.30.240:FF:000001 Ribosome maturation factor RimM
74 147 Pfam PF05239 PRC-barrel domain
74 147 InterPro IPR027275 PRC-barrel domain
76 152 SUPERFAMILY SSF50346 PRC-barrel domain
76 152 InterPro IPR011033 PRC-barrel-like superfamily
2 70 SUPERFAMILY SSF50447 Translation proteins
2 70 InterPro IPR009000 Translation protein, beta-barrel domain superfamily
1 70 Gene3D G3DSA:2.40.30.60 RimM
1 70 InterPro IPR036976 RimM, N-terminal domain superfamily
3 67 Pfam PF01782 RimM N-terminal domain
3 67 InterPro IPR002676 RimM, N-terminal
2 151 PANTHER PTHR33692 RIBOSOME MATURATION FACTOR RIMM
2 151 InterPro IPR011961 16S rRNA processing protein RimM
2 152 NCBIfam TIGR02273 ribosome maturation factor RimM
71 152 Gene3D G3DSA:2.30.30.240 -

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_A0A0H3H1R7
AlphaFold — — full sequence — Viewing
ColabFold VK055_4569
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 1.77 0.032