Protein profile

PA0807

protein AmpDh3

Genome: NC_002516.2

Gene: PA0807 ampDh3 Structure source: Experimental + AlphaFold UniProt Q9I5D1
Export view
Amino acids 255
Annotations 8
Features 17
PDB binders 2
Druggability 0.588

Overview

Basic information about this protein and its source genome.

Accession
PA0807
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0807 ampDh3
Status
annotated
Amino acids
255
Structure source
Experimental + AlphaFold
EC
3.5.1.28
GO
GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain. 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:0046872 Binding to a metal ion. GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides. 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:0009253 The chemical reactions and pathways resulting in the breakdown 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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.588
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
  • 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:0046872 Binding to a metal ion.
  • GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
  • 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:0009253 The chemical reactions and pathways resulting in the breakdown 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
173 255 Gene3D G3DSA:1.10.101.10 -
173 255 InterPro IPR036366 PGBD superfamily
7 158 SMART SM00644 ami_2
7 158 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
17 172 Gene3D G3DSA:3.40.80.10 -
17 172 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
18 160 CDD cd06583 PGRP
18 160 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
17 172 FunFam G3DSA:3.40.80.10:FF:000003 N-acetylmuramoyl-L-alanine amidase
182 253 SUPERFAMILY SSF47090 PGBD-like
182 253 InterPro IPR036365 PGBD-like superfamily
10 174 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like
10 174 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
10 248 PANTHER PTHR30417 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
17 159 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase
17 159 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain

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

Loading 3D structure...

Legend High Medium Low

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 4BXJ
X-ray 2.35 Å A,B
100.0% 1-255
PDBe RCSB PDBj File
Viewing
PDB 4BXE
X-ray 2.95 Å A,B
100.0% 1-255
PDBe RCSB PDBj File
Loaded
PDB 4BXD
X-ray 3.10 Å A,B
100.0% 1-255
PDBe RCSB PDBj File
Loaded
AlphaFold PA0807
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 3.84 0.149
2 1.47 0.02

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.

48 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
FLC
4BJ4
Q9HT86 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
J0J
4BOL
Q9HT86 461.5 Da LogP -2.66 TPSA 251.2 1 viol. ✓ Clean C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=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.