Protein profile

VK055_1974

bacterial extracellular solute-binding, 5 Middlefamily protein

Genome: KpATCC43816

Gene: AIK80580.1 Structure source: AlphaFold + ColabFold UniProt A0A9J6S657
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Amino acids 555
Annotations 5
Features 18
PDB binders 7
Druggability 0.918

Overview

Basic information about this protein and its source genome.

Accession
VK055_1974
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80580.1
Status
annotated
Amino acids
555
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:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, 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)
N
DEG identity (%)
25.7
Localization
Periplasmic
ColabFold pLDDT
93.31

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 0.918
Structure A0A9J6S657
Pocket Pocket 13
P2Rank 0.622
Structure A0A9J6S657
Pocket Pocket 1
ColabFold model
FPocket 0.808 · Pocket 23
P2Rank 0.575 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 12 / 4744 genomes with a hit
Normalized 0.003

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:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, 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.

18 records
Show feature table
Start End DB Term Name
1 32 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
13 24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
22 304 Gene3D G3DSA:3.40.190.10 -
83 471 Pfam PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
83 471 InterPro IPR000914 Solute-binding protein family 5 domain
62 546 PIRSF PIRSF002741 MppA
62 546 InterPro IPR030678 Peptide/nickel binding protein, MppA-type
25 32 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 32 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
12 545 PANTHER PTHR30290 PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
12 545 InterPro IPR039424 Solute-binding protein family 5
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 32 Phobius SIGNAL_PEPTIDE Signal peptide region
33 555 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
308 525 Gene3D G3DSA:3.10.105.10 -
31 553 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
34 538 CDD cd08495 PBP2_NikA_DppA_OppA_like_8

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_A0A9J6S657
AlphaFold — — full sequence — Viewing
ColabFold VK055_1974
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
13 0.918
6 0.493
33 0.3

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 8.83 0.473
2 8.13 0.433
3 3.94 0.155
4 1.65 0.027

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.

57 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
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)…
IUM
1B40
P06202 270.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][U+4][O-]
MHI
3O9P
P77348 390.4 Da LogP -2.17 TPSA 222.1 1 viol. ✓ Clean C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=…
MLI
3M8U
B8F653 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N72
6TFQ
O50271 309.3 Da LogP -3.46 TPSA 184.6 1 viol. ✓ Clean C(CC(=O)O)[C@H](C(=O)O)NCC(=O)[C@@H]([C@@H]([C@…
N7T
6TFS
O50271 309.3 Da LogP -3.46 TPSA 184.6 1 viol. ✓ Clean C(CC(=O)O)[C@@H](C(=O)O)NCC(=O)[C@H]([C@@H]([C@…
U1
1B05
P06202 238.0 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [U]

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.