KpATCC43816 Protein target profile

membrane-bound lytic murein transglycosylase F

Accession: VK055_4617

Gene: yfhD AIK83152.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GW83
Length 538
Pocket druggability (P2Rank · AlphaFold DB model) 0.873
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 8 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
87.06 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.873
Structure A0A0H3GW83
Pocket Pocket 1
Druggability (FPocket) 0.948
Structure A0A0H3GW83
Pocket Pocket 8
ColabFold model
P2Rank 0.878 · Pocket 1
FPocket 0.974 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 115 / 4744 genomes with a hit
Prevalence 2.4%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MPHIRRQPCVFSGHRLLRNLKLQKINSLKKLKINYLLIGIVTLLLAAALWPSIPWSGKPENRVAGIIARGELRISTINSPMTFATMNNKAFGLDYELAKQFADYLGVTLKITVRQNISQLFDDLDDGQADMLAAGLVYNQERVKNYQAGPTYYSVSQQLVYRVGNTRPRTLAALTAEQLTIAPGHVAINDLQTLKAEKYPDLAWRVDEKRGTTALMQAVIDGKLDYTIADSVAVSLFQRVHPELAVALDITDEQPVTWFSARDDDNSLSAAMLDFFNNINEDGTLARLEEKYLGHGNDFDYVDTRTFLRAVENILPEVQPLFEKYAREIDWRLLAAIAWQESHWDPQATSPTGVRGMMMLTRNTAQSLGLTDRTDAAQSIDGGMRYLQDMMDKVPDSIPKDERIWFALAAYNMGYAHMLDAMALTRKQKGNPNSWADVKLRLPLLSQKPYYSKLKYGYARGHEAYAYVENIRKYQISLVGYLSEKERQQQQTLALAEDYPAVLPNELEQPQETTLPFFKFRADKQMDNARMKLPGHLY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016837 Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
  • GO:0000270 The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only 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:0008933 Catalysis of the cleavage of a peptidoglycan chain into a peptidoglycan chain with N-acetyl-1,6-anhydromuramyl-[peptide] at the reducing end + a peptidoglycan chain with N-acetylglucosamine at the non-reducing end. Includes endolytic transglycosylase activity that fragments the glycan chain internally and exolytic transgylcosylase activity that cleaves a terminal disaccharide from the end of the glycan strand.
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0016998 The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
  • 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:0009253 The chemical reactions and pathways resulting in the breakdown 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
32 499 Hamap MF_02016 Membrane-bound lytic murein transglycosylase F [mltF].
32 499 InterPro IPR023703 Membrane-bound lytic murein transglycosylase F
156 252 Gene3D G3DSA:3.40.190.10 -
322 479 CDD cd13403 MLTF-like
70 294 CDD cd01009 PBP2_YfhD_N
337 365 ProSitePatterns PS00922 Prokaryotic transglycosylases signature.
337 365 InterPro IPR000189 Prokaryotic transglycosylase, active site
1 32 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
71 296 SMART SM00062 AABind_6
71 296 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
156 252 FunFam G3DSA:3.40.190.10:FF:000051 Membrane-bound lytic murein transglycosylase F
66 290 Gene3D G3DSA:3.40.190.10 -
33 429 PANTHER PTHR35936 MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
299 479 FunFam G3DSA:1.10.530.10:FF:000003 Membrane-bound lytic murein transglycosylase F
33 55 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 296 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
54 538 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
33 53 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
78 295 Pfam PF00497 Bacterial extracellular solute-binding proteins, family 3
78 295 InterPro IPR001638 Solute-binding protein family 3/N-terminal domain of MltF
273 468 SUPERFAMILY SSF53955 Lysozyme-like
273 468 InterPro IPR023346 Lysozyme-like domain superfamily
298 479 Gene3D G3DSA:1.10.530.10 -
324 430 Pfam PF01464 Transglycosylase SLT domain
324 430 InterPro IPR008258 Transglycosylase SLT domain 1

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.873
Likely same site as FPocket 8 5.3 Å 27 shared residues 87% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.844
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Surrounding area
Pocket 3 P2Rank #3
0.044
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Surrounding area
Pocket 4 P2Rank #4
0.039
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Surrounding area
Pocket 5 P2Rank #5
0.025
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #8
0.948 Unusual size
Likely same site as P2Rank 1 5.3 Å 27 shared residues 87% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:341-341
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GW83
AlphaFold DB full sequence Viewing
ColabFold VK055_4617
ColabFold full sequence Loaded

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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6X4 PDB via homolog 489.6 Da · LogP -3.89 · TPSA 244.7 Open detail RCSB PDB
ZINC15722130 ZINC proposed compound · Tanimoto 0.582 Detail ZINC
ZINC255987061 ZINC proposed compound · Tanimoto 0.582 Detail ZINC
ZINC255987062 ZINC proposed compound · Tanimoto 0.582 Detail ZINC
ZINC255987063 ZINC proposed compound · Tanimoto 0.582 Detail ZINC

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
6X4 RCSB PDB A0A1I9GEN8 489.6 Da LogP -3.89 TPSA 244.7 1 viol. ✓ Clean C[C@H](C(=O)N)NC(=O)C(CCCC[NH3+])NC(=O)CC[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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.