Protein profile

PA2272

penicillin-binding protein 3A

Genome: NC_002516.2

Gene: pbpC PA2272 Structure source: AlphaFold UniProt Q9I1K1
Amino acids 565
Annotations 12
Features 22
PDB binders 24
Druggability 0.369

Overview

Basic information about this protein and its source genome.

Accession
PA2272
Gene
pbpC PA2272
Status
annotated
Amino acids
565
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

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

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 0.369
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • 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:0000917 The assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis. The progeny cells that form a division septum are not able to exchange intracellular material.
  • GO:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.
  • 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:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
26 565 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
218 542 Gene3D G3DSA:3.30.450.330 -
74 142 Gene3D G3DSA:1.10.150.770 -
49 216 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
49 216 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
21 25 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
53 201 Pfam PF03717 Penicillin-binding Protein dimerisation domain
53 201 InterPro IPR005311 Penicillin-binding protein, dimerisation domain
1 558 Hamap MF_02080 Peptidoglycan D,D-transpeptidase FtsI [ftsI].
1 558 InterPro IPR037532 Peptidoglycan D,D-transpeptidase FtsI
10 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
217 545 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
217 545 InterPro IPR012338 Beta-lactamase/transpeptidase-like
23 216 Gene3D G3DSA:3.90.1310.10 -
242 538 Pfam PF00905 Penicillin binding protein transpeptidase domain
242 538 InterPro IPR001460 Penicillin-binding protein, transpeptidase
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
3 552 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE
1 25 Phobius SIGNAL_PEPTIDE Signal peptide region
278 458 Gene3D G3DSA:3.40.710.10 -
278 458 InterPro IPR012338 Beta-lactamase/transpeptidase-like

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

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA2272
AlphaFold full sequence Viewing
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 0.369
5 0.223
3 0.203

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.

75 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
0W0 Q51504 672.6 Da LogP -2.06 TPSA 328.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
3LB A0A0M3KKZ3 802.8 Da LogP -2.82 TPSA 342.9 3 viol. ✓ Clean CC(C)(C(=O)O)ON=C(c1csc(n1)N)C(=O)N[C@H](C=O)[C…
3LC A0A0M3KKZ4 788.8 Da LogP -2.41 TPSA 342.9 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
3LE A0A0M3KKZ3 776.8 Da LogP -2.57 TPSA 342.9 3 viol. ✓ Clean C[C@@H]([C@@H](C=O)NC(=O)/C(=N\OC(C)(C)C(=O)O)/…
59F Q51504 535.6 Da LogP -0.73 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
59H Q51504 463.5 Da LogP 0.04 TPSA 156.9 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
59J Q51504 549.6 Da LogP -0.36 TPSA 206.0 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
AXL G3XD46 367.4 Da LogP -0.03 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
AZR Q51504 437.5 Da LogP -1.23 TPSA 210.4 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](C=O)NC(=O)/C(=N\OC(C)(C)C(=O)O)/…
CAZ G3XD46 469.5 Da LogP 0.15 TPSA 193.6 1 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
CB9 Q51504 380.4 Da LogP 0.43 TPSA 132.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@H](c2c…
CTJ Q51504 549.6 Da LogP -0.02 TPSA 197.2 2 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
IM2 G3XD46 301.4 Da LogP -0.23 TPSA 122.5 ✓ Ro5 ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…
JPP G3XD46 519.6 Da LogP -0.29 TPSA 165.2 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C…
MER G3XD46 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
ODZ G3XD46 263.3 Da LogP 1.47 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)Cc1ccc(cc1)O
OEE G3XD46 229.3 Da LogP 1.93 TPSA 75.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)OC(C)(C)C
PFV Q51504 634.6 Da LogP -2.64 TPSA 314.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
R7G G3XD46 688.6 Da LogP -2.02 TPSA 303.5 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CN…
RB6 G3XD46 536.6 Da LogP -1.50 TPSA 212.2 3 viol. ✓ Clean C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H]…
TJ7 G3XD46 416.5 Da LogP 0.47 TPSA 142.0 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@](C=O)(NC(=O)[C@@H](c2…
UE1 G3XD46 715.7 Da LogP -5.06 TPSA 355.7 3 viol. ✓ Clean CC(C)(C(=O)[O-])O/N=C(/c1csc(n1)N)\C(=O)N[C@@H]…
VPP G3XD46 535.6 Da LogP -0.41 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C…
XT8 G3XD46 386.5 Da LogP 0.49 TPSA 132.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…

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.