Protein profile

KP13_00228

Selenocysteine-specific elongation factor

Genome: KpKP13

Gene: selB AHE42142.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUP2
Amino acids 613
Annotations 10
Features 48
PDB binders 10
Druggability 0.28

Overview

Basic information about this protein and its source genome.

Accession
KP13_00228
Gene
selB AHE42142.1
Status
annotated
Amino acids
613
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.624
Human E-value
4.8e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
43.018
DEG E-value
2.14e-177
Localization
Cytoplasmic
ColabFold pLDDT
89.11

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 0.28
Structure A0A0H3GUP2
Pocket Pocket 30
P2Rank 0.447
Structure A0A0H3GUP2
Pocket Pocket 1
ColabFold model
FPocket 0.121 · Pocket 12
P2Rank 0.46 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 102 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
  • GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0035368 Binding to a selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0016259 OBSOLETE. The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
489 547 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
489 547 InterPro IPR036390 Winged helix DNA-binding domain superfamily
549 608 FunFam G3DSA:1.10.10.10:FF:000350 Selenocysteine-specific translation elongation factor
11 173 FunFam G3DSA:3.40.50.300:FF:001064 Selenocysteine-specific translation elongation factor
418 485 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
418 485 InterPro IPR036390 Winged helix DNA-binding domain superfamily
189 256 Pfam PF03144 Elongation factor Tu domain 2
189 256 InterPro IPR004161 Translation elongation factor EFTu-like, domain 2
488 547 Gene3D G3DSA:1.10.10.10 -
488 547 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
54 64 PRINTS PR00315 GTP-binding elongation factor signature
54 64 InterPro IPR000795 Translational (tr)-type GTP-binding domain
107 116 PRINTS PR00315 GTP-binding elongation factor signature
107 116 InterPro IPR000795 Translational (tr)-type GTP-binding domain
70 81 PRINTS PR00315 GTP-binding elongation factor signature
70 81 InterPro IPR000795 Translational (tr)-type GTP-binding domain
2 15 PRINTS PR00315 GTP-binding elongation factor signature
2 15 InterPro IPR000795 Translational (tr)-type GTP-binding domain
174 260 FunFam G3DSA:2.40.30.10:FF:000080 Selenocysteine-specific translation elongation factor
425 481 Pfam PF09106 Elongation factor SelB, winged helix
425 481 InterPro IPR015190 Translation elongation factor SelB, winged helix, type 2
2 169 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
2 169 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
175 293 SUPERFAMILY SSF50447 Translation proteins
175 293 InterPro IPR009000 Translation protein, beta-barrel domain superfamily
1 608 NCBIfam TIGR00475 selenocysteine-specific translation elongation factor
1 608 InterPro IPR004535 Translation elongation factor, selenocysteine-specific
2 326 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED
1 169 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile.
1 169 InterPro IPR000795 Translational (tr)-type GTP-binding domain
552 608 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
552 608 InterPro IPR036390 Winged helix DNA-binding domain superfamily
263 337 CDD cd15491 selB_III
175 257 CDD cd03696 SelB_II
2 171 CDD cd04171 SelB
26 41 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.
26 41 InterPro IPR031157 Tr-type G domain, conserved site
548 608 Gene3D G3DSA:1.10.10.10 -
548 608 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
174 259 Gene3D G3DSA:2.40.30.10 Translation factors
275 351 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
275 351 InterPro IPR009001 Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal
2 164 Pfam PF00009 Elongation factor Tu GTP binding domain
2 164 InterPro IPR000795 Translational (tr)-type GTP-binding domain
564 606 Pfam PF09107 Elongation factor SelB, winged helix
564 606 InterPro IPR015191 Translation elongation factor SelB, winged helix, type 3
11 173 Gene3D G3DSA:3.40.50.300 -
11 173 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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_A0A0H3GUP2
AlphaFold full sequence Viewing
ColabFold KP13_00228
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
30 0.28

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 5.23 0.244
2 4.26 0.175
3 2.53 0.071
4 1.52 0.022
5 1.41 0.018

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.

60 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
1MG P0CE48 377.3 Da LogP -2.56 TPSA 195.2 1 viol. ✓ Clean CN1C(=O)c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
5GP Q8J307 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
5MU P0CE48 338.2 Da LogP -2.43 TPSA 171.3 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
DXC Q8J307 392.6 Da LogP 4.48 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
GNP O67141 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
KIR P0CE48 797.0 Da LogP 3.07 TPSA 228.1 3 viol. ✓ Clean CC[C@H](C(=O)NC\C=C\C=C(/C)\[C@H]([C@@H](C)[C@H…
PSU P0CE48 324.2 Da LogP -2.67 TPSA 182.2 1 viol. ✓ Clean C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2…
PXN P0CE48 368.5 Da LogP -0.44 TPSA 117.8 ✓ Ro5 ✓ Clean C[C@H](COCC(COC[C@@H](C)O)(COC[C@@H](C)O)COC[C@…
SEC P14081 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
Y1 Q46455 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+2]

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.