Protein profile

PA4700

penicillin-binding protein 1B

Genome: NC_002516.2

Gene: mrcB PA4700 Structure source: AlphaFold UniProt G3XD31
Amino acids 774
Annotations 12
Features 27
PDB binders 12
Druggability 0.77

Overview

Basic information about this protein and its source genome.

Accession
PA4700
Gene
mrcB PA4700
Status
annotated
Amino acids
774
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 0.77
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MTRPRSPRSRNSKARPAPGLNKWLSWALKLGLVGLVLLAGFAIYLDAVVQEKFSGRRWTIPAKVYARPLELFNGLKLSREDFLRELDALGYRREPSVSGPGTVSVAASAVELNTRGFQFYEGAEPAQRVRVRFNGNYVSGLSQANGKELAVARLEPLLIGGLYPAHHEDRILVKLDQVPTYLIDTLVAVEDRDFWNHHGVSLKSVARAVWVNTTAGQLRQGGSTLTQQLVKNFFLSNERSLSRKINEAMMAVLLELHYDKRDILESYLNEVFLGQDGQRAIHGFGLASQYFFSQPLAELKLDQVALLVGMVKGPSYFNPRRYPDRALARRNLVLDVLAEQGVATQQEVDAAKLRPLGVTRQGSMADSSYPAFLDLVKRQLRQDYRDEDLTEEGLRIFTSFDPILQEKAETSVNETLKRLSGRKGVDQVEAAMVVTNPETGEIQALIGSRDPRFAGFNRALDAVRPIGSLIKPAVYLTALERPSKYTLTTWVQDEPFAVKGQDGQVWRPQNYDRRSHGTIFLYQGLANSYNLSTAKLGLDVGVPNVLQTVARLGINRDWPAYPSMLLGAGSLSPMEVATMYQTIASGGFNTPLRGIRSVLTADGQPLKRYPFQVEQRFDSGAVYLVQNAMQRVMREGTGRSVYSQLPSSLTLAGKTGTSNDSRDSWFSGFGGDLQAVVWLGRDDNGKTPLTGATGALQVWASFMRKAHPQSLEMPMPENVVMAWVDAQTGQGSAADCPNAVQMPYIRGSEPAQGPGCGSQNPAGEVMDWVRGWLN

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

12 GO

Gene Ontology (GO)

12
  • 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:0009274 A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli.
  • 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.
  • GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
23 45 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
158 361 Gene3D G3DSA:1.10.3810.10 -
158 361 InterPro IPR036950 Penicillin binding protein transglycosylase domain
69 157 Gene3D G3DSA:3.30.2060.10 -
4 763 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
166 336 Pfam PF00912 Transglycosylase
166 336 InterPro IPR001264 Glycosyl transferase, family 51
61 725 Gene3D G3DSA:3.40.710.10 -
61 725 InterPro IPR012338 Beta-lactamase/transpeptidase-like
18 54 Gene3D G3DSA:1.20.5.100 -
23 45 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
158 361 FunFam G3DSA:1.10.3810.10:FF:000002 Penicillin-binding protein 1B
26 752 NCBIfam TIGR02071 penicillin-binding protein 1B
26 752 InterPro IPR011813 Penicillin-binding protein 1B
319 756 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
319 756 InterPro IPR012338 Beta-lactamase/transpeptidase-like
46 774 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
163 360 SUPERFAMILY SSF53955 Lysozyme-like
163 360 InterPro IPR023346 Lysozyme-like domain superfamily
431 659 Pfam PF00905 Penicillin binding protein transpeptidase domain
431 659 InterPro IPR001460 Penicillin-binding protein, transpeptidase
355 725 FunFam G3DSA:3.40.710.10:FF:000006 Penicillin-binding protein 1B
71 154 Pfam PF14814 Bifunctional transglycosylase second domain
71 154 InterPro IPR028166 Bifunctional transglycosylase second domain
1 22 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 774 PIRSF PIRSF002799 PBP1b
1 774 InterPro IPR011813 Penicillin-binding protein 1B

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 PA4700
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
4 0.77
1 0.541

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.

62 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
5VW P02919 352.4 Da LogP -2.29 TPSA 146.3 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NO[C@H…
63U P02919 349.4 Da LogP 0.39 TPSA 121.5 ✓ Ro5 ✓ Clean CC1=C(N[C@@H](SC1)[C@@H](C=O)NC(=O)[C@@H](c2ccc…
63V P02919 338.4 Da LogP 1.13 TPSA 95.8 ✓ Ro5 ✓ Clean C=C1CS[C@H](N=C1C(=O)O)[C@@H](C=O)NC(=O)Cc2cccs2
AIX P02919 351.4 Da LogP 0.26 TPSA 121.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
AZR P02919 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)/…
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-]
M0E P02919 1580.6 Da LogP -2.25 TPSA 607.7 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C…
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.