Protein profile

VK055_3704

peptidoglycan synthetase penicillin-binding protein 1A

Genome: KpATCC43816

Gene: AIK82259.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZF1
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Amino acids 811
Annotations 12
Features 23
PDB binders 11
Druggability 0.568

Overview

Basic information about this protein and its source genome.

Accession
VK055_3704
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82259.1
Status
annotated
Amino acids
811
Structure source
AlphaFold + ColabFold
EC
2.4.99.28 3.4.16.4
GO
GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. 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: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: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.

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 (%)
43.178
DEG E-value
1.88e-146
Localization
CytoplasmicMembrane
ColabFold pLDDT
88.98

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 0.568
Structure A0A0H3GZF1
Pocket Pocket 5
P2Rank 0.566
Structure A0A0H3GZF1
Pocket Pocket 1
ColabFold model
FPocket 0.11 · Pocket 33
P2Rank 0.463 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 10 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

10
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • 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: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: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: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: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.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
170 791 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
170 791 InterPro IPR012338 Beta-lactamase/transpeptidase-like
594 615 MobiDBLite mobidb-lite consensus disorder prediction
3 796 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
202 285 Gene3D G3DSA:3.40.710.10 -
202 285 InterPro IPR012338 Beta-lactamase/transpeptidase-like
388 562 Pfam PF00905 Penicillin binding protein transpeptidase domain
388 562 InterPro IPR001460 Penicillin-binding protein, transpeptidase
598 615 MobiDBLite mobidb-lite consensus disorder prediction
356 793 FunFam G3DSA:3.40.710.10:FF:000010 Penicillin-binding protein 1A
7 201 FunFam G3DSA:1.10.3810.10:FF:000003 Penicillin-binding protein 1a
14 188 Pfam PF00912 Transglycosylase
14 188 InterPro IPR001264 Glycosyl transferase, family 51
24 745 NCBIfam TIGR02074 PBP1A family penicillin-binding protein
354 793 Gene3D G3DSA:3.40.710.10 -
354 793 InterPro IPR012338 Beta-lactamase/transpeptidase-like
3 216 SUPERFAMILY SSF53955 Lysozyme-like
3 216 InterPro IPR023346 Lysozyme-like domain superfamily
202 291 FunFam G3DSA:3.40.710.10:FF:000013 Penicillin-binding protein 1A
7 201 Gene3D G3DSA:1.10.3810.10 -
7 201 InterPro IPR036950 Penicillin binding protein transglycosylase domain
275 384 Pfam PF17092 Penicillin-binding protein OB-like domain
275 384 InterPro IPR031376 Penicillin-binding protein, OB-like domain

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_A0A0H3GZF1
AlphaFold — — full sequence — Viewing
ColabFold VK055_3704
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
5 0.568

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 5.74 0.279
2 4.12 0.166
3 1.8 0.034
4 1.46 0.02
5 1.21 0.011

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.

68 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
2U4
4OON
Q07806 664.6 Da LogP -1.00 TPSA 318.0 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CO…
AZR
3UE0
G1C794 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…
IM2
3UDX
G1C794 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…
LDA
3DWK
Q8KHY3 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
PNM
3UDI
G1C794 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…
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
UE1
3UE1
G1C794 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]…

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.