Protein profile

PA2394

pyoverdine biosynthesis protein PvdN

Genome: NC_002516.2

Gene: PA2394 pvdN Structure source: Experimental + AlphaFold UniProt G3XCY5
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Amino acids 427
Annotations 5
Features 19
PDB binders 11
Druggability 0.456

Overview

Basic information about this protein and its source genome.

Accession
PA2394
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2394 pvdN
Status
annotated
Amino acids
427
Structure source
Experimental + AlphaFold
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:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine. GO:0006534 OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid. GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine. 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 (%)
28.571
Human E-value
2.16e-09
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Unknown

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 0.456
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
  • GO:0006534 OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
  • GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.
  • 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.

19 records
Show feature table
Start End DB Term Name
30 427 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
65 330 Gene3D G3DSA:3.40.640.10 -
65 330 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
40 423 SUPERFAMILY SSF53383 PLP-dependent transferases
40 423 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
22 29 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 29 Phobius SIGNAL_PEPTIDE Signal peptide region
55 419 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
55 419 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
255 275 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.
255 275 InterPro IPR020578 Aminotransferase class-V, pyridoxal-phosphate binding site
64 387 Pfam PF00266 Aminotransferase class-V
64 387 InterPro IPR000192 Aminotransferase class V domain
1 31 ProSiteProfiles PS51318 Twin arginine translocation (Tat) signal profile.
1 31 InterPro IPR006311 Twin-arginine translocation pathway, signal sequence
11 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
40 422 PANTHER PTHR43586 CYSTEINE DESULFURASE

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 5I90
X-ray 1.22 Å A,B
100.0% 1-427
PDBe RCSB PDBj File
Viewing
PDB 5HH9
X-ray 1.47 Å A,B
91.3% 38-427
PDBe RCSB PDBj File
Loaded
AlphaFold PA2394
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 0.456
5 0.263

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 22.02 0.876
2 3.56 0.132
3 3.47 0.126
4 2.27 0.057
5 2.1 0.048

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
7TS
7CES
O32164 331.2 Da LogP 0.60 TPSA 157.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CONC2=O)O
8QJ
5V12
A7UX13 246.3 Da LogP 0.68 TPSA 86.2 ✓ Ro5 ✓ Clean C[N+](C)(C)[C@@H](Cc1c[nH]c(n1)SO)C(=O)O
8VV
5V1X
A7UX13 333.4 Da LogP -1.37 TPSA 146.4 ✓ Ro5 ✓ Clean C[N+](C)(C)[C@@H](Cc1c[nH]c(n1)[S@](=O)C[C@@H](…
C6P
5ZSO
O32164 352.3 Da LogP 0.18 TPSA 149.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CS)C(=O)O)O
CKT
6O13
P77444 350.3 Da LogP 0.66 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CS)/C(=O)O)O
DCS
7CER
O32164 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
LPG
1I29
P77444 99.1 Da LogP -0.97 TPSA 63.3 ✓ Ro5 ✓ Clean C#CC(C(=O)O)N
PDA
5XT6
O32164 320.2 Da LogP 0.27 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O
PLR
3GZC
Q96I15 233.2 Da LogP 1.01 TPSA 99.9 ✓ Ro5 ✓ Clean Cc1c(cnc(c1O)C)COP(=O)(O)O
PMP
7CEO
O32164 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SEC
1KMK
P77444 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]

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.