Protein profile

VK055_2523

exported protein required for envelope biosynthesis and integrity

Genome: KpATCC43816

Gene: AIK81120.1 lptD Structure source: Experimental + ColabFold UniProt C4T9I0
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Amino acids 740
Annotations 7
Features 8
PDB binders 3
Druggability 0.656

Overview

Basic information about this protein and its source genome.

Accession
VK055_2523
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81120.1 lptD
Status
annotated
Amino acids
740
Structure source
Experimental + ColabFold
GO
GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. GO:0061024 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide. GO:0010033 OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.

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 (%)
81.586
DEG E-value
0.0
Localization
OuterMembrane
ColabFold pLDDT
93.23

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 0.656
Structure 5IV8
Pocket Pocket 20
P2Rank 0.875
Structure 5IV8
Pocket Pocket 1
ColabFold model
FPocket 0.962 · Pocket 63
P2Rank 0.906 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 112 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0061024 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
  • GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
  • GO:0010033 OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
  • GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:1990351 A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

8 records
Show feature table
Start End DB Term Name
7 719 Hamap MF_01411 LPS-assembly protein LptD [lptD].
7 719 InterPro IPR020889 LPS-assembly protein LptD
6 160 Gene3D G3DSA:2.60.450.10 Lipopolysaccharide (LPS) transport protein A like domain
267 651 Pfam PF04453 LPS transport system D
267 651 InterPro IPR007543 LptD, C-terminal
11 152 Pfam PF03968 LptA/(LptD N-terminal domain) LPS transport protein
11 152 InterPro IPR005653 Organic solvent tolerance-like, N-terminal
6 736 PANTHER PTHR30189 LPS-ASSEMBLY 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

2 + 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 5IV8
X-ray 2.94 Å A,C
72.7% 203-740
PDBe RCSB PDBj File
Viewing
PDB 5IV9
X-ray 4.37 Å A
96.8% 25-740
PDBe RCSB PDBj File
Loaded
ColabFold VK055_2523
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
103 0.819
13 0.636
29 0.464
113 0.268

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 29.04 0.929
2 27.2 0.919
3 24.46 0.899
4 22.53 0.881
5 21.91 0.875

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.

53 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
C8E
5IV9 4.37 Å Open crystal
306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO

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.