Protein profile

KP13_00227

L-seryl-tRNA(Sec) selenium transferase

Genome: KpKP13

Gene: selA AHE42141.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H014
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Amino acids 462
Annotations 6
Features 16
PDB binders 1
Druggability 0.321

Overview

Basic information about this protein and its source genome.

Accession
KP13_00227
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
selA AHE42141.1
Status
annotated
Amino acids
462
Structure source
AlphaFold + ColabFold
EC
2.9.1.1
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004125 Catalysis of the reaction: L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + H2O + phosphate. 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:0001514 The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine. GO:0001717 The modification process that results in the conversion of serine, carried by a specialized tRNA(ser) (which can read a UGA anticodon), to selenocysteine.

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
94.72

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 0.321
Structure A0A0H3H014
Pocket Pocket 6
P2Rank 0.845
Structure A0A0H3H014
Pocket Pocket 1
ColabFold model
FPocket 0.517 · Pocket 22
P2Rank 0.804 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004125 Catalysis of the reaction: L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + H2O + phosphate.
  • 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:0001514 The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
  • GO:0001717 The modification process that results in the conversion of serine, carried by a specialized tRNA(ser) (which can read a UGA anticodon), to selenocysteine.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 462 Hamap MF_00423 L-seryl-tRNA(Sec) selenium transferase [selA].
1 462 InterPro IPR004534 L-seryl-tRNA(Sec) selenium transferase
9 460 PANTHER PTHR32328 L-SERYL-TRNA(SEC) SELENIUM TRANSFERASE
78 381 SUPERFAMILY SSF53383 PLP-dependent transferases
78 381 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
37 57 Coils Coil Coil
80 451 Gene3D G3DSA:3.90.1150.180 -
10 459 NCBIfam TIGR00474 L-seryl-tRNA(Sec) selenium transferase
10 459 InterPro IPR004534 L-seryl-tRNA(Sec) selenium transferase
11 48 Pfam PF12390 Selenocysteine synthase N terminal
11 48 InterPro IPR025862 L-seryl-tRNA selenium transferase N-terminal domain
83 450 Pfam PF03841 L-seryl-tRNA selenium transferase
83 450 InterPro IPR018319 L-seryl-tRNA selenium transferase-like
95 358 FunFam G3DSA:3.40.640.10:FF:000028 L-seryl-tRNA(Sec) selenium transferase
95 358 Gene3D G3DSA:3.40.640.10 -
95 358 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major 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

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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_A0A0H3H014
AlphaFold — — full sequence — Viewing
ColabFold KP13_00227
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
6 0.321

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 11.35 0.607
2 2.65 0.078
3 0.76 0.002

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.

1 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
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.