Overview
Basic information about this protein and its source genome.
- Accession
- VK055_3113
- Gene
- rplA AIK81694.1
- Status
- annotated
- Amino acids
- 234
- Structure source
- AlphaFold + ColabFold
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 (%)
- 98.291
- DEG E-value
- 6.220000000000001e-167
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 85.49
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
8- GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
- GO:0003723 Binding to an RNA molecule or a portion thereof.
- GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
- GO:0015934 The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
- GO:0022625 The large subunit of a ribosome located in the cytosol.
- GO:0019843 Binding to a ribosomal RNA.
- GO:0000049 Binding to a transfer RNA.
- GO:0006417 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 121 | 139 | ProSitePatterns | PS01199 | Ribosomal protein L1 signature. |
| 121 | 139 | InterPro | IPR023673 | Ribosomal protein L1, conserved site |
| 68 | 159 | FunFam | G3DSA:3.40.50.790:FF:000001 | 50S ribosomal protein L1 |
| 30 | 219 | Pfam | PF00687 | Ribosomal protein L1p/L10e family |
| 30 | 219 | InterPro | IPR028364 | Ribosomal protein L1/ribosomal biogenesis protein |
| 1 | 227 | PIRSF | PIRSF002155 | RPL1p_RPL1a_RPL10e_RPL1o |
| 1 | 227 | InterPro | IPR002143 | Ribosomal protein L1 |
| 2 | 229 | Hamap | MF_01318_B | 50S ribosomal protein L1 [rplA]. |
| 2 | 229 | InterPro | IPR005878 | Ribosomal protein L1, bacterial-type |
| 13 | 226 | PANTHER | PTHR36427 | 54S RIBOSOMAL PROTEIN L1, MITOCHONDRIAL |
| 23 | 224 | CDD | cd00403 | Ribosomal_L1 |
| 23 | 224 | InterPro | IPR028364 | Ribosomal protein L1/ribosomal biogenesis protein |
| 21 | 225 | Gene3D | G3DSA:3.30.190.20 | - |
| 3 | 227 | NCBIfam | TIGR01169 | 50S ribosomal protein L1 |
| 3 | 227 | InterPro | IPR005878 | Ribosomal protein L1, bacterial-type |
| 68 | 159 | Gene3D | G3DSA:3.40.50.790 | - |
| 68 | 159 | InterPro | IPR016095 | Ribosomal protein L1, 3-layer alpha/beta-sandwich |
| 6 | 225 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 |
| 6 | 225 | InterPro | IPR023674 | Ribosomal protein L1-like |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GKI9
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_3113
|
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 | 0.001 | ||||||
| 2 | 0.001 | ||||||
| 3 | 0.001 | ||||||
| 7 | 0.001 |
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 | 0.409 | ||||||
| 2 | 0.004 | ||||||
| 4 | 0.001 | ||||||
| 7 | 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 | 1.39 | 0.014 |
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| MLI | P27150 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
|
| PTL | P54050 | 86.1 Da LogP 1.38 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCCC=O
|
|
| TLA | P54050 | 150.1 Da LogP -2.12 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
[C@@H]([C@H](C(=O)O)O)(C(=O)O)O
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1693894 | 0.765 | 212.4 Da LogP 4.89 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC=O
|
| ZINC13546064 | 0.737 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCC/C=C\CCCCCCCC=O
|
| ZINC1850393 | 0.737 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCC/C=C/CCCCCCCC=O
|
| ZINC12359024 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC13533920 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1532740 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC1549593 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC2013424 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC3581021 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC3860635 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC5783661 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC6072527 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC43061660 | 0.650 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCCCC/C=C\CCCCCC=O
|
| ZINC43061664 | 0.650 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CCCCCC/C=C/CCCCCC=O
|
| ZINC1560405156 | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC1560405157 | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC1529331 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529332 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O
|
| ZINC1529333 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529334 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O
|
| ZINC2569627 | 0.500 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CC/C=C/CCCCCCCCCC=O
|
| ZINC33949609 | 0.500 | 210.4 Da LogP 4.66 TPSA 17.1 | ✓ Ro5 | ✓ Clean |
CC/C=C\CCCCCCCCCC=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.