Protein profile

KP13_31867

Glycine betaine-binding periplasmic protein

Genome: KpKP13

Gene: proX AHE43075.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GX45
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Amino acids 332
Annotations 3
Features 13
PDB binders 2
Druggability 0.858

Overview

Basic information about this protein and its source genome.

Accession
KP13_31867
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
proX AHE43075.1
Status
annotated
Amino acids
332
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:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. 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
94.07

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 0.858
Structure A0A0H3GX45
Pocket Pocket 1
P2Rank 0.662
Structure A0A0H3GX45
Pocket Pocket 1
ColabFold model
FPocket 0.815 · Pocket 1
P2Rank 0.638 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 115 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • 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.

13 records
Show feature table
Start End DB Term Name
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
114 255 Gene3D G3DSA:3.40.190.100 -
31 314 Pfam PF04069 Substrate binding domain of ABC-type glycine betaine transport system
31 314 InterPro IPR007210 ABC-type glycine betaine transport system, substrate-binding domain
26 324 CDD cd13638 PBP2_EcProx_like
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
25 330 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
25 327 Gene3D G3DSA:3.40.190.10 -
7 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
23 332 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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_A0A0H3GX45
AlphaFold — — full sequence — Viewing
ColabFold KP13_31867
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 0.858

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 12.53 0.654
2 2.26 0.056
3 1.06 0.007

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.

4 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
BET
3TMG
O51169 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
PBE
1R9Q
P0AFM2 144.2 Da LogP 0.31 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+]1(CCC[C@H]1C(=O)O)C

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.