Protein profile

PA3487

phospholipase D

Genome: NC_002516.2

Gene: PA3487 pldA Structure source: Experimental + AlphaFold UniProt Q9HYC2
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Amino acids 1099
Annotations 4
Features 20
PDB binders 2
Druggability 0.924

Overview

Basic information about this protein and its source genome.

Accession
PA3487
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3487 pldA
Status
annotated
Amino acids
1099
Structure source
Experimental + AlphaFold
GO
GO:0046872 Binding to a metal ion. GO:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid. GO:0009395 The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
38.728
Human E-value
6.1800000000000006e-27
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Periplasmic

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 0.924
Structure –
Pocket –

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:0046872 Binding to a metal ion.
  • GO:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid.
  • GO:0009395 The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1080 1099 MobiDBLite mobidb-lite consensus disorder prediction
164 189 Pfam PF00614 Phospholipase D Active site motif
164 189 InterPro IPR001736 Phospholipase D/Transphosphatidylase
851 877 Pfam PF00614 Phospholipase D Active site motif
851 877 InterPro IPR001736 Phospholipase D/Transphosphatidylase
162 189 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile.
162 189 InterPro IPR001736 Phospholipase D/Transphosphatidylase
41 971 PANTHER PTHR18896 PHOSPHOLIPASE D
41 971 InterPro IPR015679 Phospholipase D family
40 209 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
428 512 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
46 495 SUPERFAMILY SSF56024 Phospholipase D/nuclease
850 877 SMART SM00155 pld_4
850 877 InterPro IPR001736 Phospholipase D/Transphosphatidylase
162 189 SMART SM00155 pld_4
606 925 SUPERFAMILY SSF56024 Phospholipase D/nuclease
600 894 CDD cd09141 PLDc_vPLD1_2_yPLD_like_2
561 901 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A
850 877 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile.
51 200 CDD cd09104 PLDc_vPLD1_2_like_1

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 7V53
X-ray 2.10 Å A
100.0% 1-1099
PDBe RCSB PDBj File
Viewing
PDB 7V55
X-ray 3.00 Å A
100.0% 1-1099
PDBe RCSB PDBj File
Loaded
AlphaFold PA3487
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
1 0.517
6 0.208

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 24.77 0.901
2 9.31 0.5
3 7.09 0.368
4 6.92 0.356
5 6.24 0.312

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.

152 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
DTT
6OHO
O14939 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
WO4
6OHM
O14939 247.8 Da LogP -2.62 TPSA 80.3 ✓ Ro5 ✓ Clean [O-][W](=O)(=O)[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.