Protein profile

PA4559

lipoprotein signal peptidase

Genome: NC_002516.2

Gene: ls PA4559 lspA Structure source: Experimental + AlphaFold UniProt Q9HVM5
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Amino acids 169
Annotations 7
Features 33
PDB binders 3
Druggability 0.927

Overview

Basic information about this protein and its source genome.

Accession
PA4559
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
ls PA4559 lspA
Status
annotated
Amino acids
169
Structure source
Experimental + AlphaFold
EC
3.4.23.36
GO
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0004190 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile. GO:0004175 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain. GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

Selected Druggability evidence

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 0.927
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0004190 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
  • GO:0004175 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
  • GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
89 94 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
115 133 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
96 118 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 28 SignalP_EUK SignalP-noTM SignalP-noTM
8 164 Hamap MF_00161 Lipoprotein signal peptidase [lspA].
8 164 InterPro IPR001872 Peptidase A8, signal peptidase II
95 114 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
10 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
67 89 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
10 164 PANTHER PTHR33695 LIPOPROTEIN SIGNAL PEPTIDASE
10 164 InterPro IPR001872 Peptidase A8, signal peptidase II
68 88 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
133 155 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
16 158 Pfam PF01252 Signal peptidase (SPase) II
16 158 InterPro IPR001872 Peptidase A8, signal peptidase II
31 41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
102 117 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
102 117 InterPro IPR001872 Peptidase A8, signal peptidase II
139 155 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
139 155 InterPro IPR001872 Peptidase A8, signal peptidase II
54 62 PRINTS PR00781 Lipoprotein signal peptidase family (A8) signature
54 62 InterPro IPR001872 Peptidase A8, signal peptidase II
105 117 ProSitePatterns PS00855 Signal peptidases II signature.
105 117 InterPro IPR001872 Peptidase A8, signal peptidase II
12 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
10 162 NCBIfam TIGR00077 signal peptidase II
10 162 InterPro IPR001872 Peptidase A8, signal peptidase II
156 169 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
41 63 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
42 62 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
63 67 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
134 155 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

3 + 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 5DIR
X-ray 2.80 Å A,B,C,D
100.0% 1-169
PDBe RCSB PDBj File
Viewing
PDB 9EMZ
X-ray 3.00 Å A,B,C,D
100.0% 1-169
PDBe RCSB PDBj File
Loaded
PDB 6FMS
X-ray 3.00 Å A,B,C,D
99.4% 2-169
PDBe RCSB PDBj File
Loaded
AlphaFold PA4559
AlphaFold — — 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
2 0.927
4 0.273

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 8.78 0.47
2 1.35 0.016

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
OLC
5DIR 2.80 Å Open crystal
356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.