Protein profile

PA5198

LD-carboxypeptidase

Genome: NC_002516.2

Gene: PA5198 Structure source: Experimental + AlphaFold UniProt Q9HTZ1
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Amino acids 307
Annotations 9
Features 17
PDB binders 8
Druggability 0.573

Overview

Basic information about this protein and its source genome.

Accession
PA5198
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA5198
Status
annotated
Amino acids
307
Structure source
Experimental + AlphaFold
EC
3.4.17.13
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0106415 GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H2O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine. GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides. GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

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 0.573
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0106415 GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H2O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine.
  • GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
14 143 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
14 143 InterPro IPR029062 Class I glutamine amidotransferase-like
18 134 Pfam PF02016 LD-carboxypeptidase N-terminal domain
18 134 InterPro IPR040449 LD-carboxypeptidase, N-terminal
18 298 CDD cd07025 Peptidase_S66
185 299 Pfam PF17676 LD-carboxypeptidase C-terminal domain
185 299 InterPro IPR040921 LD-carboxypeptidase, C-terminal
10 304 PANTHER PTHR30237 MURAMOYLTETRAPEPTIDE CARBOXYPEPTIDASE
10 304 InterPro IPR003507 Peptidase family S66
13 307 PIRSF PIRSF028757 LD-carboxypeptidase
13 307 InterPro IPR003507 Peptidase family S66
1 170 Gene3D G3DSA:3.40.50.10740 -
1 170 InterPro IPR027478 Murein tetrapeptide carboxypeptidase, N-terminal
171 307 Gene3D G3DSA:3.50.30.60 -
171 307 InterPro IPR027461 LD-carboxypeptidase A, C-terminal domain superfamily
157 304 SUPERFAMILY SSF141986 LD-carboxypeptidase A C-terminal domain-like
157 304 InterPro IPR027461 LD-carboxypeptidase A, C-terminal domain superfamily

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

4 + 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 1ZL0
X-ray 1.10 Å A,B
100.0% 1-307
PDBe RCSB PDBj File
Viewing
PDB 1ZRS
X-ray 1.50 Å A,B
100.0% 1-307
PDBe RCSB PDBj File
Loaded
PDB 2AUM
X-ray 2.40 Å A,B
100.0% 1-307
PDBe RCSB PDBj File
Loaded
PDB 2AUN
X-ray 2.40 Å A,B
100.0% 1-307
PDBe RCSB PDBj File
Loaded
AlphaFold PA5198
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
3 0.573
6 0.412
2 0.269

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 18.87 0.831
2 3.19 0.109
3 3.17 0.108
4 3.05 0.101
5 2.91 0.093

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

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
TLA
1ZL0 1.10 Å Open crystal
150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.