Protein profile

VK055_0217

protein-(glutamine-N5) methyltransferase, release factor-specific

Genome: KpATCC43816

Gene: prmC AIK78845.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPQ1
Export view
Amino acids 282
Annotations 7
Features 21
PDB binders 6
Druggability 0.929

Overview

Basic information about this protein and its source genome.

Accession
VK055_0217
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
prmC AIK78845.1
Status
annotated
Amino acids
282
Structure source
AlphaFold + ColabFold
EC
2.1.1.297
GO
GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GO:0003676 Binding to a nucleic acid. GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein. 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. GO:0102559 Catalysis of the reaction: L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-methionine = N(5)-methyl-L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-homocysteine + H+.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.889
Human E-value
2.32e-17
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
75.182
DEG E-value
1.4299999999999998e-150
Localization
Cytoplasmic
ColabFold pLDDT
94.9

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 0.929
Structure A0A0H3GPQ1
Pocket Pocket 1
P2Rank 0.733
Structure A0A0H3GPQ1
Pocket Pocket 1
ColabFold model
FPocket 0.293 · Pocket 2
P2Rank 0.742 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein.
  • 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.
  • GO:0102559 Catalysis of the reaction: L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-methionine = N(5)-methyl-L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-homocysteine + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
3 275 Hamap MF_02126 Release factor glutamine methyltransferase [prmC].
3 275 InterPro IPR019874 Protein-(glutamine-N5) methyltransferase, release factor-specific
7 274 PANTHER PTHR18895 HEMK METHYLTRANSFERASE
85 276 FunFam G3DSA:3.40.50.150:FF:000053 Release factor glutamine methyltransferase
4 273 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
4 273 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
110 246 Pfam PF13847 Methyltransferase domain
110 246 InterPro IPR025714 Methyltransferase domain
23 271 NCBIfam TIGR03534 peptide chain release factor N(5)-glutamine methyltransferase
23 271 InterPro IPR019874 Protein-(glutamine-N5) methyltransferase, release factor-specific
2 275 NCBIfam TIGR00536 HemK family protein methyltransferase
2 275 InterPro IPR004556 Methyltransferase HemK-like
1 83 FunFam G3DSA:1.10.8.10:FF:000032 Release factor glutamine methyltransferase
112 237 CDD cd02440 AdoMet_MTases
85 275 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
85 275 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1 83 Gene3D G3DSA:1.10.8.10 -
180 186 ProSitePatterns PS00092 N-6 Adenine-specific DNA methylases signature.
180 186 InterPro IPR002052 DNA methylase, N-6 adenine-specific, conserved site
6 73 Pfam PF17827 PrmC N-terminal domain
6 73 InterPro IPR040758 Release factor glutamine methyltransferase, N-terminal domain

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_A0A0H3GPQ1
AlphaFold — — full sequence — Viewing
ColabFold VK055_0217
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 0.929

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 9.5 0.511
2 8.7 0.465
3 0.88 0.004

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.

56 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
7QM
5U1I
Q2MG72 497.5 Da LogP -7.06 TPSA 274.4 2 viol. ✓ Clean CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)O[C@H]2[C…
7XP
5U0N
Q2MG72 454.5 Da LogP -6.65 TPSA 262.4 2 viol. ✓ Clean C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…
827
5U19
Q2MG72 482.5 Da LogP -6.00 TPSA 248.4 2 viol. ✓ Clean C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…
9CS
5U1E
Q2MG72 483.5 Da LogP -7.33 TPSA 288.4 2 viol. ✓ Clean C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…
GET
5U18
Q2MG72 496.6 Da LogP -5.61 TPSA 248.4 2 viol. ✓ Clean C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@…
MEQ
1NV8
Q9WYV8 160.2 Da LogP -1.08 TPSA 92.4 ✓ Ro5 ✓ Clean CNC(=O)CC[C@@H](C(=O)O)N

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.