Protein profile

VK055_1479

fe(3+)-binding periplasmic protein

Genome: KpATCC43816

Gene: fbpA AIK80100.1 Structure source: Experimental + ColabFold UniProt A0A060VGH4
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Amino acids 338
Annotations 4
Features 17
PDB binders 4
Druggability 0.406

Overview

Basic information about this protein and its source genome.

Accession
VK055_1479
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
fbpA AIK80100.1
Status
annotated
Amino acids
338
Structure source
Experimental + ColabFold
GO
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:0046872 Binding to a metal ion. GO:0006826 The directed movement of iron (Fe) ions 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 (%)
37.013
Localization
Periplasmic
ColabFold pLDDT
93.09

Selected Druggability evidence

PDB experimental structure

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 0.406
Structure 8K7N
Pocket Pocket 1
P2Rank 0.523
Structure 8K7N
Pocket Pocket 1
ColabFold model
FPocket 0.505 · Pocket 1
P2Rank 0.55 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 36 / 4744 genomes with a hit
Normalized 0.008

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: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:0046872 Binding to a metal ion.
  • GO:0006826 The directed movement of iron (Fe) ions 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.

17 records
Show feature table
Start End DB Term Name
126 143 ProSitePatterns PS01037 Bacterial extracellular solute-binding proteins, family 1 signature.
126 143 InterPro IPR006061 Solute-binding family 1, conserved site
128 313 Gene3D G3DSA:3.40.190.10 -
1 26 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 336 PANTHER PTHR30006 THIAMINE-BINDING PERIPLASMIC PROTEIN-RELATED
33 327 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
81 308 Pfam PF13343 Bacterial extracellular solute-binding protein
22 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 27 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
32 337 CDD cd13543 PBP2_Fbp
27 338 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
34 308 Gene3D G3DSA:3.40.190.10 -
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 338 PIRSF PIRSF002825 CfbpA
1 338 InterPro IPR026045 Ferric binding protein

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 8K7N
X-ray 2.00 Å A
100.0% 1-338
PDBe RCSB PDBj File
Viewing
ColabFold VK055_1479
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 0.406

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 9.74 0.523
2 1.88 0.037
3 1.58 0.025
4 1.47 0.02
5 0.9 0.004

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
EDT
1NNF
P35755 292.2 Da LogP -2.07 TPSA 155.7 ✓ Ro5 ✓ Clean C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
FLC
6G7Q
Q10Z45 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
OXL
2OWS
Q7VXW9 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
ZRC
1XC1
P17259 576.6 Da LogP -10.44 TPSA 282.7 2 viol. ✓ Clean [O-][Zr]123(OP4(=O)O[Zr]5(O1)([O+]2[Zr](O4)(O3)…

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.