Protein profile

KP13_01631

tRNA (mo5U34)-methyltransferase

Genome: KpKP13

Gene: cmoB AHE43847.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H064
Export view
Amino acids 334
Annotations 5
Features 13
PDB binders 3
Druggability 0.744

Overview

Basic information about this protein and its source genome.

Accession
KP13_01631
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
cmoB AHE43847.1
Status
annotated
Amino acids
334
Structure source
AlphaFold + ColabFold
EC
2.5.1.-
GO
GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon. GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor). GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0032259 The process in which a methyl group is covalently attached to a molecule.

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 (%)
84.211
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.06

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 0.744
Structure A0A0H3H064
Pocket Pocket 20
P2Rank 0.905
Structure A0A0H3H064
Pocket Pocket 1
ColabFold model
FPocket 0.322 · Pocket 2
P2Rank 0.924 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 151 / 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.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
12 322 Hamap MF_01590 tRNA U34 carboxymethyltransferase [cmoB].
12 322 InterPro IPR010017 tRNA U34 carboxymethyltransferase
95 323 FunFam G3DSA:3.40.50.150:FF:000080 tRNA U34 carboxymethyltransferase
99 318 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
99 318 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
7 322 Pfam PF08003 Protein of unknown function (DUF1698)
7 322 InterPro IPR027555 tRNA (Mo5U34)-methyltransferase-like
7 321 NCBIfam TIGR00452 tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB
7 321 InterPro IPR010017 tRNA U34 carboxymethyltransferase
91 323 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
91 323 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
30 230 PANTHER PTHR43464 METHYLTRANSFERASE
125 229 CDD cd02440 AdoMet_MTases

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...

Legend High Medium Low

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_A0A0H3H064
AlphaFold — — full sequence — Viewing
ColabFold KP13_01631
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
20 0.744

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 20.63 0.859

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
BTB
4P7C
Q87XG5 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
GEK
4QNU
A1AC32 442.5 Da LogP -5.85 TPSA 227.2 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
MLI
7CT9
Q8DAP0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]

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.