Protein profile

VK055_4011

undecaprenyl-diphosphatase UppP

Genome: KpATCC43816

Gene: uppP AIK82558.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVS2
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Amino acids 273
Annotations 9
Features 35
PDB binders 2
Druggability 0.843

Overview

Basic information about this protein and its source genome.

Accession
VK055_4011
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
uppP AIK82558.1
Status
annotated
Amino acids
273
Structure source
AlphaFold + ColabFold
EC
3.6.1.27
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0016311 The process of removing one or more phosphoric (ester or anhydride) residues from a molecule. GO:0050380 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate. 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: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.

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 (%)
45.936
DEG E-value
6.59e-72
Localization
CytoplasmicMembrane
ColabFold pLDDT
95.65

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 0.843
Structure A0A0H3GVS2
Pocket Pocket 7
P2Rank 0.882
Structure A0A0H3GVS2
Pocket Pocket 1
ColabFold model
FPocket 0.882 · Pocket 11
P2Rank 0.812 · 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 8 GO

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:0016311 The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
  • GO:0050380 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate.
  • 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: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: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.

35 records
Show feature table
Start End DB Term Name
273 273 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
247 251 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
173 191 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
224 246 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 18 SignalP_EUK SignalP-TM SignalP-TM
90 110 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
214 224 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
111 121 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
90 112 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
122 139 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
10 265 NCBIfam TIGR00753 undecaprenyl-diphosphatase UppP
10 265 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
14 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
252 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
225 246 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
50 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
141 151 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 272 Hamap MF_01006 Undecaprenyl-diphosphatase [uppP].
5 272 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
122 140 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
70 89 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 49 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
187 209 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
192 213 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 272 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
50 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
152 172 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 272 PANTHER PTHR30622 UNDECAPRENYL-DIPHOSPHATASE
6 272 InterPro IPR003824 Undecaprenyl-diphosphatase UppP
10 266 Pfam PF02673 Bacitracin resistance protein BacA
10 266 InterPro IPR003824 Undecaprenyl-diphosphatase UppP

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_A0A0H3GVS2
AlphaFold — — full sequence — Viewing
ColabFold VK055_4011
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 0.843

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 16.93 0.791
2 2.68 0.08
3 1.9 0.038
4 1.79 0.033
5 1.42 0.018

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.

52 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
FLC
6FMV
P60932 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
OLC
5OON
P60932 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O

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.