Protein profile

VK055_2825

cys/Met metabolism PLP-dependent enzyme family protein

Genome: KpATCC43816

Gene: AIK81414.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMG8
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Amino acids 372
Annotations 2
Features 10
PDB binders 6
Druggability 0.29

Overview

Basic information about this protein and its source genome.

Accession
VK055_2825
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81414.1
Status
annotated
Amino acids
372
Structure source
AlphaFold + ColabFold
GO
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:0004125 Catalysis of the reaction: L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + H2O + phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.24

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 0.29
Structure A0A0H3GMG8
Pocket Pocket 7
P2Rank 0.902
Structure A0A0H3GMG8
Pocket Pocket 1
ColabFold model
FPocket 0.545 · Pocket 25
P2Rank 0.939 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 127 / 4744 genomes with a hit
Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • 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:0004125 Catalysis of the reaction: L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + H2O + phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
4 368 PANTHER PTHR32328 L-SERYL-TRNA(SEC) SELENIUM TRANSFERASE
14 269 Pfam PF03841 L-seryl-tRNA selenium transferase
14 269 InterPro IPR018319 L-seryl-tRNA selenium transferase-like
23 275 Gene3D G3DSA:3.40.640.10 -
23 275 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
6 368 SUPERFAMILY SSF53383 PLP-dependent transferases
6 368 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
4 365 NCBIfam TIGR01437 DgaE family pyridoxal phosphate-dependent ammonia lyase
4 365 InterPro IPR006337 D-glucosaminate-6-phosphate ammonia lyase DgaE-like
23 274 FunFam G3DSA:3.40.640.10:FF:000056 SelA-like pyridoxal phosphate-dependent enzyme

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_A0A0H3GMG8
AlphaFold — — full sequence — Viewing
ColabFold VK055_2825
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
7 0.29
2 0.063
1 0.004
5 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 30.18 0.902
2 2.3 0.048
3 1.6 0.021
4 1.14 0.008

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
3LM
5X2W
P13254 378.3 Da LogP 1.13 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN/C(=C/CSC)/C(=O)O)O
4LM
5X2X
P13254 330.2 Da LogP 1.11 TPSA 149.5 ✓ Ro5 ✓ Clean C/C=C(\C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O
7XF
5X30
P13254 366.3 Da LogP 0.57 TPSA 149.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCS)C(=O)O)O
H2S
5X2X
P13254 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
HCS
3VK4
P13254 135.2 Da LogP -0.28 TPSA 63.3 ✓ Ro5 ✓ Clean C(CS)[C@@H](C(=O)O)N
THJ
3W1J
O67140 112.1 Da LogP -1.01 TPSA 57.2 ✓ Ro5 ✓ Clean [O-]S(=O)(=O)[S-]

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.