Protein profile

KP13_02857

Autoinducer 2-binding protein lsrB

Genome: KpKP13

Gene: AHE42574.1 lsrB Structure source: AlphaFold + ColabFold UniProt A0A0H3GTJ1
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Amino acids 333
Annotations 4
Features 16
PDB binders 3
Druggability 0.369

Overview

Basic information about this protein and its source genome.

Accession
KP13_02857
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42574.1 lsrB
Status
annotated
Amino acids
333
Structure source
AlphaFold + ColabFold
GO
GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. 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. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

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
Periplasmic
ColabFold pLDDT
95.37

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 0.369
Structure A0A0H3GTJ1
Pocket Pocket 2
P2Rank 0.109
Structure A0A0H3GTJ1
Pocket Pocket 1
ColabFold model
FPocket 0.544 · Pocket 1
P2Rank 0.317 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 59 / 4744 genomes with a hit
Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • 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.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
22 329 CDD cd20003 PBP1_LsrB_Quorum_Sensing
22 329 InterPro IPR030159 Autoinducer 2 ABC transporter, substrate-binding protein LsrB
22 317 Gene3D G3DSA:3.40.50.2300 -
5 332 PANTHER PTHR30036 D-XYLOSE-BINDING PERIPLASMIC PROTEIN
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
123 333 Gene3D G3DSA:3.40.50.2300 -
16 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
5 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
23 278 Pfam PF13407 Periplasmic binding protein domain
23 278 InterPro IPR025997 Periplasmic binding protein
21 333 SUPERFAMILY SSF53822 Periplasmic binding protein-like I
21 333 InterPro IPR028082 Periplasmic binding protein-like I
20 333 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
1 19 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.

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

Loading 3D structure...

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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_A0A0H3GTJ1
AlphaFold — — full sequence — Viewing
ColabFold KP13_02857
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
2 0.369
1 0.225

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 3.51 0.129

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.

53 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
PAV
4PZ0
A0A6H3AKG3 150.1 Da LogP -2.23 TPSA 90.2 ✓ Ro5 ✓ Clean C[C@@]1(C([C@H](CO1)O)(O)O)O
RIP
7E7M
Q8E283 150.1 Da LogP -2.58 TPSA 90.2 ✓ Ro5 ✓ Clean C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
TLZ
4RY9
A1WJM2 182.2 Da LogP -3.59 TPSA 121.4 1 viol. ✓ Clean C([C@H]([C@H]([C@H]([C@@H](CO)O)O)O)O)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.