Protein profile

KP13_04583

Penicillin-binding protein 2

Genome: KpKP13

Gene: AHE44458.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GY10
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Amino acids 655
Annotations 10
Features 23
PDB binders 4
Druggability 0.074

Overview

Basic information about this protein and its source genome.

Accession
KP13_04583
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44458.1
Status
annotated
Amino acids
655
Structure source
AlphaFold + ColabFold
EC
3.4.16.4
GO
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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine. 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:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 D-alanine.

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 (%)
59.588
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
88.74

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 0.074
Structure A0A0H3GY10
Pocket Pocket 29
P2Rank 0.525
Structure A0A0H3GY10
Pocket Pocket 1
ColabFold model
FPocket 0.14 · Pocket 35
P2Rank 0.456 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 132 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 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.

23 records
Show feature table
Start End DB Term Name
274 634 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
274 634 InterPro IPR012338 Beta-lactamase/transpeptidase-like
39 634 NCBIfam TIGR03423 penicillin-binding protein 2
39 634 InterPro IPR017790 Penicillin-binding protein 2
63 655 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
268 642 FunFam G3DSA:3.40.710.10:FF:000004 Peptidoglycan D,D-transpeptidase MrdA
268 646 Gene3D G3DSA:3.40.710.10 -
268 646 InterPro IPR012338 Beta-lactamase/transpeptidase-like
84 257 Pfam PF03717 Penicillin-binding Protein dimerisation domain
84 257 InterPro IPR005311 Penicillin-binding protein, dimerisation domain
42 64 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
292 631 Pfam PF00905 Penicillin binding protein transpeptidase domain
292 631 InterPro IPR001460 Penicillin-binding protein, transpeptidase
105 180 Gene3D G3DSA:3.30.1390.30 -
23 638 Hamap MF_02081 Peptidoglycan D,D-transpeptidase MrdA [mrdA].
23 638 InterPro IPR017790 Penicillin-binding protein 2
36 637 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE
1 40 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
41 62 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 273 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
77 273 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
84 267 Gene3D G3DSA:3.90.1310.10 -
174 268 FunFam G3DSA:3.90.1310.10:FF:000001 Peptidoglycan D,D-transpeptidase MrdA

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 + 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_A0A0H3GY10
AlphaFold — — full sequence — Viewing
ColabFold KP13_04583
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 6.24 0.312
2 2.68 0.079
3 1.72 0.03
4 1.2 0.01

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.

60 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
ET5
6G9S
P0AD65 334.3 Da LogP -0.93 TPSA 168.2 ✓ Ro5 ✓ Clean c1c(ocn1)C2=C[C@H](N(C[C@@H]2NOS(=O)(=O)O)C(=O)…
JPP
6H5O
A0A0H3JPA5 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…
NXL
6G9F
P0AD65 267.3 Da LogP -2.21 TPSA 139.0 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
RB6
6G88
Q47759 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]…

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.