Protein profile

KP13_00785

Putative ribosome maturation factor rimN

Genome: KpKP13

Gene: AHE42398.1 rimN Structure source: AlphaFold + ColabFold UniProt A0A0H3GTZ8
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Amino acids 190
Annotations 8
Features 11
PDB binders 3
Druggability 0.598

Overview

Basic information about this protein and its source genome.

Accession
KP13_00785
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42398.1 rimN
Status
annotated
Amino acids
190
Structure source
AlphaFold + ColabFold
EC
2.7.7.87
GO
GO:0002949 The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base). GO:0003725 Binding to double-stranded RNA. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0061710 Catalysis of the reaction: L-threonine + hydrogencarbonate + ATP = L-threonylcarbamoyladenylate + diphosphate + H2O. GO:0000049 Binding to a transfer RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.624
Human E-value
6.36e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
82.105
DEG E-value
2.63e-115
Localization
Cytoplasmic
ColabFold pLDDT
94.26

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 0.598
Structure A0A0H3GTZ8
Pocket Pocket 1
P2Rank 0.399
Structure A0A0H3GTZ8
Pocket Pocket 1
ColabFold model
FPocket 0.408 · Pocket 9
P2Rank 0.49 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 143 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0002949 The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
  • GO:0003725 Binding to double-stranded RNA.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0061710 Catalysis of the reaction: L-threonine + hydrogencarbonate + ATP = L-threonylcarbamoyladenylate + diphosphate + H2O.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0006450 Any process that modulates the ability of the translational apparatus to interpret the genetic code.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
16 190 Pfam PF01300 Telomere recombination
16 190 InterPro IPR006070 Threonylcarbamoyl-AMP synthase-like domain
1 188 Gene3D G3DSA:3.90.870.10 DHBP synthase
7 190 ProSiteProfiles PS51163 YrdC-like domain profile.
7 190 InterPro IPR006070 Threonylcarbamoyl-AMP synthase-like domain
5 187 SUPERFAMILY SSF55821 YrdC/RibB
5 187 InterPro IPR017945 DHBP synthase RibB-like alpha/beta domain superfamily
1 188 FunFam G3DSA:3.90.870.10:FF:000004 Threonylcarbamoyl-AMP synthase
7 188 Hamap MF_01852 Threonylcarbamoyl-AMP synthase [tsaC].
7 188 InterPro IPR023535 Threonylcarbamoyl-AMP synthase
7 190 PANTHER PTHR17490 SUA5

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

Loading 3D structure...

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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_A0A0H3GTZ8
AlphaFold — — full sequence — Viewing
ColabFold KP13_00785
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 0.598

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 5.47 0.261
2 4.43 0.187

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.

53 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
ANP
3AJE
Q970S6 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
POP
6F87
Q9UYB2 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
TXA
4E1B
Q970S6 492.3 Da LogP -2.30 TPSA 261.7 2 viol. ✓ Clean C[C@H]([C@@H](C(=O)O)NC(=O)OP(=O)(O)OC[C@@H]1[C…

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.