Protein profile

KP13_01829

Penicillin-binding protein 1B

Genome: KpKP13

Gene: AHE46269.1 mrcB Structure source: AlphaFold + ColabFold UniProt A0A0H3GIH5
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Amino acids 850
Annotations 12
Features 32
PDB binders 12
Druggability 0.761

Overview

Basic information about this protein and its source genome.

Accession
KP13_01829
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46269.1 mrcB
Status
annotated
Amino acids
850
Structure source
AlphaFold + ColabFold
GO
GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. 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: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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
47.908
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
86.71

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 0.761
Structure A0A0H3GIH5
Pocket Pocket 15
P2Rank 0.723
Structure A0A0H3GIH5
Pocket Pocket 1
ColabFold model
FPocket 0.603 · Pocket 10
P2Rank 0.785 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 109 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

12 GO

Gene Ontology (GO)

12
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • 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: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: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: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.
  • 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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
209 380 Pfam PF00912 Transglycosylase
209 380 InterPro IPR001264 Glycosyl transferase, family 51
201 404 FunFam G3DSA:1.10.3810.10:FF:000002 Penicillin-binding protein 1B
196 403 SUPERFAMILY SSF53955 Lysozyme-like
196 403 InterPro IPR023346 Lysozyme-like domain superfamily
111 200 Gene3D G3DSA:3.30.2060.10 -
65 87 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
46 835 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
795 834 MobiDBLite mobidb-lite consensus disorder prediction
201 404 Gene3D G3DSA:1.10.3810.10 -
201 404 InterPro IPR036950 Penicillin binding protein transglycosylase domain
1 56 MobiDBLite mobidb-lite consensus disorder prediction
87 850 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
65 86 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
113 197 Pfam PF14814 Bifunctional transglycosylase second domain
113 197 InterPro IPR028166 Bifunctional transglycosylase second domain
1 79 Pfam PF14812 Transmembrane domain of transglycosylase PBP1 at N-terminal
1 79 InterPro IPR032730 Transglycosylase PBP1b, N-terminal transmembrane domain
58 96 Gene3D G3DSA:1.20.5.100 -
398 767 FunFam G3DSA:3.40.710.10:FF:000006 Penicillin-binding protein 1B
473 713 Pfam PF00905 Penicillin binding protein transpeptidase domain
473 713 InterPro IPR001460 Penicillin-binding protein, transpeptidase
68 792 NCBIfam TIGR02071 penicillin-binding protein 1B
68 792 InterPro IPR011813 Penicillin-binding protein 1B
1 64 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
103 767 Gene3D G3DSA:3.40.710.10 -
103 767 InterPro IPR012338 Beta-lactamase/transpeptidase-like
795 850 MobiDBLite mobidb-lite consensus disorder prediction
362 788 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
362 788 InterPro IPR012338 Beta-lactamase/transpeptidase-like
36 848 PIRSF PIRSF002799 PBP1b
36 848 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.

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_A0A0H3GIH5
AlphaFold — — full sequence — Viewing
ColabFold KP13_01829
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
15 0.761
36 0.214

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 14.21 0.715
2 5.51 0.263
3 2.79 0.086
4 1.85 0.036
5 1.73 0.031

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
5FGZ
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
5HLA
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
5HLD
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
5HL9
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
5HLB
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
2ZC5
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
3ZGA
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
3ZG9
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
3DWK
Q8KHY3 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
M0E
3FWL
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
2ZC6
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
3ZG7
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.