Protein profile

VK055_0673

penicillin-binding protein 2

Genome: KpATCC43816

Gene: AIK79296.1 mrdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GY10
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Amino acids 636
Annotations 10
Features 23
PDB binders 4
Druggability 0.074

Overview

Basic information about this protein and its source genome.

Accession
VK055_0673
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79296.1 mrdA
Status
annotated
Amino acids
636
Structure source
AlphaFold + ColabFold
EC
3.4.16.4
GO
GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine. 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: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
90.14

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 0.105 · Pocket 42
P2Rank 0.54 · Pocket 1
Core conservation Accessory gene
Roary core
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:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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: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
4 619 Hamap MF_02081 Peptidoglycan D,D-transpeptidase MrdA [mrdA].
4 619 InterPro IPR017790 Penicillin-binding protein 2
273 612 Pfam PF00905 Penicillin binding protein transpeptidase domain
273 612 InterPro IPR001460 Penicillin-binding protein, transpeptidase
249 627 Gene3D G3DSA:3.40.710.10 -
249 627 InterPro IPR012338 Beta-lactamase/transpeptidase-like
65 238 Pfam PF03717 Penicillin-binding Protein dimerisation domain
65 238 InterPro IPR005311 Penicillin-binding protein, dimerisation domain
65 248 Gene3D G3DSA:3.90.1310.10 -
17 618 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE
249 623 FunFam G3DSA:3.40.710.10:FF:000004 Peptidoglycan D,D-transpeptidase MrdA
58 254 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
58 254 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
255 615 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
255 615 InterPro IPR012338 Beta-lactamase/transpeptidase-like
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
21 43 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
44 636 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
86 161 Gene3D G3DSA:3.30.1390.30 -
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
155 249 FunFam G3DSA:3.90.1310.10:FF:000001 Peptidoglycan D,D-transpeptidase MrdA
20 615 NCBIfam TIGR03423 penicillin-binding protein 2
20 615 InterPro IPR017790 Penicillin-binding protein 2

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 VK055_0673
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.