Protein profile

KP13_03339

Penicillin-binding protein 2

Genome: KpKP13

Gene: AHE45718.1 mrdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GTX1
Amino acids 633
Annotations 10
Features 24
PDB binders 25
Druggability 0.315

Overview

Basic information about this protein and its source genome.

Accession
KP13_03339
Gene
AHE45718.1 mrdA
Status
annotated
Amino acids
633
Structure source
AlphaFold + ColabFold

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 (%)
93.207
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
90.36

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 0.315
Structure A0A0H3GTX1
Pocket Pocket 7
P2Rank 0.724
Structure A0A0H3GTX1
Pocket Pocket 1
ColabFold model
FPocket 0.137 · Pocket 7
P2Rank 0.916 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Normalized 0.031

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.

24 records
Show feature table
Start End DB Term Name
3 616 Hamap MF_02081 Peptidoglycan D,D-transpeptidase MrdA [mrdA].
3 616 InterPro IPR017790 Penicillin-binding protein 2
64 239 Pfam PF03717 Penicillin-binding Protein dimerisation domain
64 239 InterPro IPR005311 Penicillin-binding protein, dimerisation domain
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
64 248 Gene3D G3DSA:3.90.1310.10 -
249 619 Gene3D G3DSA:3.40.710.10 -
249 619 InterPro IPR012338 Beta-lactamase/transpeptidase-like
254 611 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
254 611 InterPro IPR012338 Beta-lactamase/transpeptidase-like
15 619 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE
152 248 FunFam G3DSA:3.90.1310.10:FF:000001 Peptidoglycan D,D-transpeptidase MrdA
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
85 160 FunFam G3DSA:3.30.1390.30:FF:000001 Peptidoglycan D,D-transpeptidase MrdA
41 633 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
19 612 NCBIfam TIGR03423 penicillin-binding protein 2
19 612 InterPro IPR017790 Penicillin-binding protein 2
85 160 Gene3D G3DSA:3.30.1390.30 -
56 253 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
56 253 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
248 620 FunFam G3DSA:3.40.710.10:FF:000004 Peptidoglycan D,D-transpeptidase MrdA
272 609 Pfam PF00905 Penicillin binding protein transpeptidase domain
272 609 InterPro IPR001460 Penicillin-binding protein, transpeptidase

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_A0A0H3GTX1
AlphaFold full sequence Viewing
ColabFold KP13_03339
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
7 0.315

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 7.29 0.38
2 2.53 0.071
3 2.33 0.06
4 1.69 0.029
5 1.25 0.012

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.

79 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
0W0 Q51504 672.6 Da LogP -2.06 TPSA 328.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
59F Q51504 535.6 Da LogP -0.73 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
59H Q51504 463.5 Da LogP 0.04 TPSA 156.9 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
59J Q51504 549.6 Da LogP -0.36 TPSA 206.0 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
AI8 Q9K3C9 607.7 Da LogP 1.24 TPSA 185.7 2 viol. ✓ Clean CCON=C(c1nc(sn1)N)C(=O)N[C@H](C=O)[C@@H]2NC(=C(…
AXL G3XD46 367.4 Da LogP -0.03 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
AZR Q51504 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)/…
CAZ G3XD46 469.5 Da LogP 0.15 TPSA 193.6 1 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
CB9 Q51504 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…
CTJ Q51504 549.6 Da LogP -0.02 TPSA 197.2 2 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
ET5 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)…
IM2 A0A075Q0W3 301.4 Da LogP -0.23 TPSA 122.5 ✓ Ro5 ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…
JPP G3XD46 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…
MER G3XD46 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
NXL 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
ODZ G3XD46 263.3 Da LogP 1.47 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)Cc1ccc(cc1)O
OEE G3XD46 229.3 Da LogP 1.93 TPSA 75.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)OC(C)(C)C
PFV Q51504 634.6 Da LogP -2.64 TPSA 314.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
PNM A0A075Q0W3 336.4 Da LogP 0.81 TPSA 95.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2…
R7G G3XD46 688.6 Da LogP -2.02 TPSA 303.5 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CN…
RB6 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]…
TJ7 G3XD46 416.5 Da LogP 0.47 TPSA 142.0 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@](C=O)(NC(=O)[C@@H](c2…
UE1 G3XD46 715.7 Da LogP -5.06 TPSA 355.7 3 viol. ✓ Clean CC(C)(C(=O)[O-])O/N=C(/c1csc(n1)N)\C(=O)N[C@@H]…
VPP G3XD46 535.6 Da LogP -0.41 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C…
XT8 G3XD46 386.5 Da LogP 0.49 TPSA 132.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…

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.