Protein profile

VK055_4651

penicillin-binding protein 1C

Genome: KpATCC43816

Gene: pbpC AIK83185.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H1G6
Amino acids 771
Annotations 7
Features 26
PDB binders 8
Druggability 0.635

Overview

Basic information about this protein and its source genome.

Accession
VK055_4651
Gene
pbpC AIK83185.1
Status
annotated
Amino acids
771
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
38.514
Localization
CytoplasmicMembrane
ColabFold pLDDT
90.04

Selected Druggability evidence

AlphaFold / UniProt model

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 0.635
Structure A0A0H3H1G6
Pocket Pocket 9
P2Rank 0.405
Structure A0A0H3H1G6
Pocket Pocket 1
ColabFold model
FPocket 0.562 · Pocket 21
P2Rank 0.303 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 100 / 4744 genomes with a hit
Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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: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: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:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
248 592 FunFam G3DSA:3.40.710.10:FF:000021 Penicillin-binding protein 1C
10 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
21 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
685 765 Pfam PF06832 Penicillin-Binding Protein C-terminus Family
685 765 InterPro IPR009647 Penicillin-binding, C-terminal
25 771 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
52 246 Gene3D G3DSA:1.10.3810.10 -
52 246 InterPro IPR036950 Penicillin binding protein transglycosylase domain
249 574 Gene3D G3DSA:3.40.710.10 -
249 574 InterPro IPR012338 Beta-lactamase/transpeptidase-like
9 566 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
38 255 SUPERFAMILY SSF53955 Lysozyme-like
38 255 InterPro IPR023346 Lysozyme-like domain superfamily
299 515 Pfam PF00905 Penicillin binding protein transpeptidase domain
299 515 InterPro IPR001460 Penicillin-binding protein, transpeptidase
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
53 247 FunFam G3DSA:1.10.3810.10:FF:000006 Penicillin-binding protein 1C
35 769 NCBIfam TIGR02073 penicillin-binding protein 1C
35 769 InterPro IPR011815 Penicillin-binding protein 1C
205 639 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
205 639 InterPro IPR012338 Beta-lactamase/transpeptidase-like
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 25 SignalP_EUK SignalP-noTM SignalP-noTM
57 223 Pfam PF00912 Transglycosylase
57 223 InterPro IPR001264 Glycosyl transferase, family 51

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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3H1G6
AlphaFold full sequence Viewing
ColabFold VK055_4651
ColabFold 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
46 0.143
1 0.005
40 0.001
47 0.0

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 8.83 0.405
2 3.56 0.106
3 2.99 0.078
4 2.19 0.043
5 1.79 0.028

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.

65 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
2U4 Q07806 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…
35P P71707 352.4 Da LogP 0.64 TPSA 104.7 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)COc2ccccc…
BMG Q04707 352.4 Da LogP -1.95 TPSA 111.2 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@@H]2Cn3cnc[n+]3C2)C(=O…
CB9 Q8Y547 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…
DXF Q8Y547 426.4 Da LogP -0.59 TPSA 182.6 ✓ Ro5 ✓ Clean CO/N=C(/c1ccco1)\C(=O)N[C@H](C=O)[C@@H]2NC(=C(C…
LDA Q8KHY3 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
TEB Q04707 385.5 Da LogP 0.61 TPSA 102.2 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1SC2CN(C2)C3=NCCS3)C(=O)O)[…
TLA Q8Y547 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.