Protein profile

VK055_1664

bacterial extracellular solute-binding, 5 Middlefamily protein

Genome: KpATCC43816

Gene: AIK80284.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKG5
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Amino acids 513
Annotations 5
Features 21
PDB binders 4
Druggability 0.733

Overview

Basic information about this protein and its source genome.

Accession
VK055_1664
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80284.1
Status
annotated
Amino acids
513
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:0055085 The process in which a solute 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:1904680 Enables the transfer of a peptide from one side of a membrane to the other. GO:0042938 The directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

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 (%)
87.476
DEG E-value
0.0
Localization
Periplasmic
ColabFold pLDDT
93.9

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 0.733
Structure A0A0H3GKG5
Pocket Pocket 1
P2Rank 0.617
Structure A0A0H3GKG5
Pocket Pocket 1
ColabFold model
FPocket 0.686 · Pocket 1
P2Rank 0.535 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 106 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0055085 The process in which a solute 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:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • GO:0042938 The directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
262 486 Gene3D G3DSA:3.10.105.10 -
186 269 FunFam G3DSA:3.40.190.10:FF:000094 Glutathione ABC transporter substrate-binding protein GsiB
37 185 Gene3D G3DSA:3.90.76.10 -
1 26 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
27 513 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
37 185 FunFam G3DSA:3.90.76.10:FF:000003 Glutathione ABC transporter substrate-binding protein GsiB
186 496 Gene3D G3DSA:3.40.190.10 -
71 428 Pfam PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
71 428 InterPro IPR000914 Solute-binding protein family 5 domain
29 507 CDD cd08499 PBP2_Ylib_like
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
13 512 PIRSF PIRSF002741 MppA
13 512 InterPro IPR030678 Peptide/nickel binding protein, MppA-type
18 508 PANTHER PTHR30290 PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
18 508 InterPro IPR039424 Solute-binding protein family 5
269 486 FunFam G3DSA:3.10.105.10:FF:000003 Glutathione ABC transporter substrate-binding protein GsiB
22 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
30 509 SUPERFAMILY SSF53850 Periplasmic binding protein-like II

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_A0A0H3GKG5
AlphaFold — — full sequence — Viewing
ColabFold VK055_1664
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 0.733
2 0.528

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 8.46 0.452
2 7.25 0.378
3 4.94 0.223
4 3.55 0.131
5 2.57 0.073

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.

54 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
G9Z
6HLX
O50260 291.3 Da LogP -3.73 TPSA 158.8 1 viol. ✓ Clean C1=CC(=O)N([C@@H]1C(=O)O)C[C@H]([C@H]([C@@H]([C…
GDS
3M8U
B8F653 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
MLI
3M8U
B8F653 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OXL
4OEV
Q0P844 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=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.