Protein profile

VK055_4814

lysine-arginine-ornithine-binding periplasmic family protein

Genome: KpATCC43816

Gene: AIK83341.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWD2
Export view
Amino acids 247
Annotations 3
Features 14
PDB binders 8
Druggability 0.166

Overview

Basic information about this protein and its source genome.

Accession
VK055_4814
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83341.1
Status
annotated
Amino acids
247
Structure source
AlphaFold + ColabFold
GO
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: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:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, 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 (%)
34.764
Localization
Periplasmic
ColabFold pLDDT
95.88

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 0.166
Structure A0A0H3GWD2
Pocket Pocket 3
P2Rank 0.034
Structure A0A0H3GWD2
Pocket Pocket 1
ColabFold model
FPocket 0.506 · Pocket 1
P2Rank 0.056 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 98 / 4744 genomes with a hit
Normalized 0.021

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: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: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:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, 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.

14 records
Show feature table
Start End DB Term Name
14 243 SMART SM00062 AABind_6
14 243 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
2 240 NCBIfam TIGR01096 lysine/arginine/ornithine ABC transporter substrate-binding protein
2 240 InterPro IPR005768 Specific amino acids and opine-binding periplasmic protein, ABC transporter
37 50 ProSitePatterns PS01039 Bacterial extracellular solute-binding proteins, family 3 signature.
37 50 InterPro IPR018313 Solute-binding protein family 3, conserved site
13 244 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
12 240 CDD cd13703 PBP2_HisJ_LAO
13 240 PANTHER PTHR35936 MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
100 200 FunFam G3DSA:3.40.190.10:FF:000020 Histidine ABC transporter substrate-binding periplasmic protein
15 241 Pfam PF00497 Bacterial extracellular solute-binding proteins, family 3
15 241 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
100 200 Gene3D G3DSA:3.40.190.10 -
16 239 Gene3D G3DSA:3.40.190.10 -

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GWD2
AlphaFold — — full sequence — Viewing
ColabFold VK055_4814
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 1.27 0.013

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.

58 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
2W2
5OVZ
P35120 304.3 Da LogP -1.39 TPSA 185.8 1 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](CCC(=O)O)C…
6DB
5ITO
P35120 246.3 Da LogP -1.23 TPSA 148.5 1 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O
AOZ
5OT9
P35120 227.2 Da LogP -0.53 TPSA 115.3 ✓ Ro5 ✓ Clean CC(C(=O)O)NC(Cc1c[nH]cn1)C(=O)O
AQK
5OTC
P35120 190.2 Da LogP -1.15 TPSA 112.7 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)NCC(=O)O)CN
AQQ
5OTA
P35120 204.2 Da LogP -0.76 TPSA 112.6 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)N[C@@H](CCCN)C(=O)O
OP1
4POW
P35120 286.3 Da LogP -1.22 TPSA 156.8 ✓ Ro5 ✓ Clean [H]/N=C(\N)/NCCC[C@@H](C(=O)O)N1[C@H](CCC1=O)C(…
ORN
1LAH
P02911 132.2 Da LogP -0.86 TPSA 89.3 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CN
TOE
5ITO
P35120 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO

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.