Protein profile
KP13_01642
L-arabinose-binding periplasmic protein
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_01642
- Gene
- AHE43836.1 araF
- Status
- annotated
- Amino acids
- 326
- 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 (%)
- 91.718
- DEG E-value
- 0.0
- Localization
- Periplasmic
- ColabFold pLDDT
- 94.69
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)
3- GO:0042882 The process in which L-arabinose, the L-enantiomer of arabinose, is transported across a lipid bilayer, from one side of a membrane to the other.
- GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
- GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 326 | PIRSF | PIRSF002816 | AraF |
| 1 | 326 | InterPro | IPR026266 | L-arabinose-binding periplasmic protein |
| 27 | 321 | CDD | cd01540 | PBP1_arabinose_binding |
| 27 | 321 | InterPro | IPR026266 | L-arabinose-binding periplasmic protein |
| 24 | 326 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 26 | 319 | Pfam | PF00532 | Periplasmic binding proteins and sugar binding domain of LacI family |
| 26 | 319 | InterPro | IPR001761 | Periplasmic binding protein/LacI sugar binding domain |
| 26 | 324 | SUPERFAMILY | SSF53822 | Periplasmic binding protein-like I |
| 26 | 324 | InterPro | IPR028082 | Periplasmic binding protein-like I |
| 27 | 308 | Gene3D | G3DSA:3.40.50.2300 | - |
| 1 | 23 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 1 | 23 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 132 | 317 | Gene3D | G3DSA:3.40.50.2300 | - |
| 1 | 23 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 1 | 6 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 27 | 162 | FunFam | G3DSA:3.40.50.2300:FF:000075 | L-arabinose-binding periplasmic protein |
| 7 | 18 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 19 | 23 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 1 | 320 | PANTHER | PTHR30036 | D-XYLOSE-BINDING PERIPLASMIC PROTEIN |
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_A0A0H3GQ80
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_01642
|
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 |
|---|---|---|---|---|---|---|---|
| 4 | 0.247 | ||||||
| 5 | 0.033 | ||||||
| 14 | 0.016 | ||||||
| 6 | 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 | 5.35 | 0.208 | ||||||
| 2 | 1.42 | 0.015 |
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 |
|---|---|---|---|---|---|---|---|
| 8 | 0.518 | ||||||
| 2 | 0.278 | ||||||
| 7 | 0.013 | ||||||
| 6 | 0.001 |
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 | 7.12 | 0.31 |
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.
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 |
|---|---|---|---|---|---|
| ZINC4097487 | 0.500 | 326.3 Da LogP -4.37 TPSA 169.3 | 1 viol. | ✓ Clean |
C[C@@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H…
|
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.