Protein profile

KP13_04184

peptidoglycan binding-like protein

Genome: KpKP13

Gene: AHE45415.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GR14
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Amino acids 596
Annotations 5
Features 24
PDB binders 1
Druggability 0.077

Overview

Basic information about this protein and its source genome.

Accession
KP13_04184
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45415.1
Status
annotated
Amino acids
596
Structure source
AlphaFold + ColabFold
GO
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GO:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain. 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:0008360 Any process that modulates the surface configuration of a cell.

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 (%)
0.0
Localization
Periplasmic
ColabFold pLDDT
86.65

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 0.077
Structure A0A0H3GR14
Pocket Pocket 14
P2Rank 0.837
Structure A0A0H3GR14
Pocket Pocket 1
ColabFold model
FPocket 0.585 · Pocket 2
P2Rank 0.793 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 98 / 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.

5 GO

Gene Ontology (GO)

5
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.
  • 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:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
1 30 Phobius SIGNAL_PEPTIDE Signal peptide region
358 524 Pfam PF03734 L,D-transpeptidase catalytic domain
358 524 InterPro IPR005490 L,D-transpeptidase catalytic domain
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
241 331 Gene3D G3DSA:1.10.101.10 -
241 331 InterPro IPR036366 PGBD superfamily
1 30 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
23 30 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
358 523 CDD cd16913 YkuD_like
358 523 InterPro IPR005490 L,D-transpeptidase catalytic domain
11 22 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 594 PANTHER PTHR41533 L,D-TRANSPEPTIDASE HI_1667-RELATED
238 336 SUPERFAMILY SSF47090 PGBD-like
238 336 InterPro IPR036365 PGBD-like superfamily
352 525 Gene3D G3DSA:2.40.440.10 -
352 525 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
356 514 SUPERFAMILY SSF141523 L,D-transpeptidase catalytic domain-like
356 514 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
98 228 Pfam PF20142 Scaffold domain
98 228 InterPro IPR045380 L,D-transpeptidase, scaffold domain
254 329 Pfam PF01471 Putative peptidoglycan binding domain
254 329 InterPro IPR002477 Peptidoglycan binding-like
1 30 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
31 596 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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_A0A0H3GR14
AlphaFold — — full sequence — Viewing
ColabFold KP13_04184
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 16.17 0.772
2 10.96 0.588
3 6.24 0.313
4 4.4 0.185
5 4.32 0.179

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.

1 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
MXR
6NTW
P22525 385.5 Da LogP -0.35 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…

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.