Protein profile

KP13_04246

ABC transporter arginine-binding protein 1

Genome: KpKP13

Gene: AHE45478.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GM56
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Amino acids 243
Annotations 4
Features 24
PDB binders 1
Druggability 0.607

Overview

Basic information about this protein and its source genome.

Accession
KP13_04246
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45478.1
Status
annotated
Amino acids
243
Structure source
AlphaFold + ColabFold
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 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:0015276 Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

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 (%)
45.714
DEG E-value
1.16e-71
Localization
Periplasmic
ColabFold pLDDT
93.71

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 0.607
Structure A0A0H3GM56
Pocket Pocket 1
P2Rank 0.129
Structure A0A0H3GM56
Pocket Pocket 1
ColabFold model
FPocket 0.24 · Pocket 3
P2Rank 0.091 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 122 / 4744 genomes with a hit
Normalized 0.026

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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0071705 The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • 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:0015276 Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 19 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
1 19 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
108 201 Gene3D G3DSA:3.40.190.10 -
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
22 243 SMART SM00079 GluR_14
22 243 InterPro IPR001320 Ionotropic glutamate receptor, C-terminal
25 240 Gene3D G3DSA:3.40.190.10 -
1 242 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
22 243 SMART SM00062 AABind_6
22 243 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
23 242 Pfam PF00497 Bacterial extracellular solute-binding proteins, family 3
23 242 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
6 242 PANTHER PTHR35936 MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
21 243 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
108 201 FunFam G3DSA:3.40.190.10:FF:000014 Arginine ABC transporter substrate-binding protein
20 241 CDD cd13700 PBP2_Arg_STM4351
45 58 ProSitePatterns PS01039 Bacterial extracellular solute-binding proteins, family 3 signature.
45 58 InterPro IPR018313 Solute-binding protein family 3, conserved site
4 241 NCBIfam TIGR01096 lysine/arginine/ornithine ABC transporter substrate-binding protein
4 241 InterPro IPR005768 Specific amino acids and opine-binding periplasmic protein, ABC transporter

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_A0A0H3GM56
AlphaFold — — full sequence — Viewing
ColabFold KP13_04246
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 0.019
4 0.001
3 0.0
10 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 3.98 0.129
2 1.52 0.018
3 1.36 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.

51 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
ORN
1LAH
P02911 132.2 Da LogP -0.86 TPSA 89.3 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CN

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.