Protein profile

PA5045

penicillin-binding protein 1A

Genome: NC_002516.2

Gene: mrcA ponA PA5045 Structure source: Experimental + AlphaFold UniProt Q07806
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Amino acids 822
Annotations 10
Features 30
PDB binders 12
Druggability 0.566

Overview

Basic information about this protein and its source genome.

Accession
PA5045
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
mrcA ponA PA5045
Status
annotated
Amino acids
822
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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. GO:0008955 Catalysis of the reaction: [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H+. GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine. 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.

Target profile

Computed evidence for target prioritization.

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

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 0.566
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0008955 Catalysis of the reaction: [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H+.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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: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.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
55 229 Pfam PF00912 Transglycosylase
55 229 InterPro IPR001264 Glycosyl transferase, family 51
211 801 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
211 801 InterPro IPR012338 Beta-lactamase/transpeptidase-like
790 822 MobiDBLite mobidb-lite consensus disorder prediction
428 605 Pfam PF00905 Penicillin binding protein transpeptidase domain
428 605 InterPro IPR001460 Penicillin-binding protein, transpeptidase
648 741 Pfam PF00905 Penicillin binding protein transpeptidase domain
648 741 InterPro IPR001460 Penicillin-binding protein, transpeptidase
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 29 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
43 255 SUPERFAMILY SSF53955 Lysozyme-like
43 255 InterPro IPR023346 Lysozyme-like domain superfamily
1 6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
243 323 Gene3D G3DSA:3.40.710.10 -
243 323 InterPro IPR012338 Beta-lactamase/transpeptidase-like
631 792 Gene3D G3DSA:3.40.710.10 -
631 792 InterPro IPR012338 Beta-lactamase/transpeptidase-like
400 621 Gene3D G3DSA:3.40.710.10 -
400 621 InterPro IPR012338 Beta-lactamase/transpeptidase-like
316 420 Pfam PF17092 Penicillin-binding protein OB-like domain
316 420 InterPro IPR031376 Penicillin-binding protein, OB-like domain
604 654 MobiDBLite mobidb-lite consensus disorder prediction
48 242 FunFam G3DSA:1.10.3810.10:FF:000003 Penicillin-binding protein 1a
30 822 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
48 242 Gene3D G3DSA:1.10.3810.10 -
48 242 InterPro IPR036950 Penicillin binding protein transglycosylase domain
3 800 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
65 751 NCBIfam TIGR02074 PBP1A family penicillin-binding protein
243 329 FunFam G3DSA:3.40.710.10:FF:000042 Penicillin-binding protein 1A

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

1 + 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 4OON
X-ray 3.20 Å A
95.7% 36-822
PDBe RCSB PDBj File
Viewing
AlphaFold PA5045
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
5 0.566
13 0.49

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 1.65 0.027
2 1.6 0.025
3 1.31 0.014

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.

69 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
2U4
4OON 3.20 Å Open crystal
664.6 Da LogP -1.00 TPSA 318.0 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CO…

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.