Protein profile

PA1636

two-component sensor KdpD

Genome: NC_002516.2

Gene: PA1636 kdpD Structure source: AlphaFold UniProt Q9I389
Amino acids 885
Annotations 12
Features 60
PDB binders 4
Druggability 0.671

Overview

Basic information about this protein and its source genome.

Accession
PA1636
Gene
PA1636 kdpD
Status
annotated
Amino acids
885
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
CytoplasmicMembrane

Selected Druggability evidence

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 0.671
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MTDTARADALLADLPADGRGRLKVFLGAAPGVGKTFAMLQAAQAQLRQGVKLRAGVVETHSRAETESLLAGVPQQPLRSLEYRGMKLQEMDLDGLLADPPALALVDELAHSNVPGSRHAKRWQDIQELLAAGIDVYTTVNVQHLESLNDQVRDITGVQVRETVPDWVLQEAYEIVLIDLPPRELLERLREGKVYVPEQARAAIDAFFSQTNLTALRELAMQTAAARVDADLNHRYRQRGEEAPALRGRLLVGIDGDEQAERLVRHACRVAERRHLPWSVVHVDTGGLRGEQARMRLQGAQQLAERLGGEIVVLRAGEVARTLLQHARERRASLVLVGQSRRRWYRRAFGGGLAGRLLRDGQGLEISALDSEADLRPAEPRPRYPVVWNDYLLALLATALASGLAWIVAHLLELPNISLVFLMAVLLVAVRSSLMPALLCAVASFLAYDFLFIPPHFSFAIHRHEDLLSLAFFLFMAGLTGNLAARQRRQLEALRDTQEETSLLLELSRKLTAATDRQAVLAAAAQQFDDWKDVEVCLLGQVNGEWKTEAGVQRQLADQERVAADWAWAHDQPAGLGTGTLPGGRWWWWPLSAEEGPLALLGVAPLDGQPLSPQRRRLLAALGQPLAQALARARLAEDLEAARLHGETEQLRSALLASVSHDLRTPLTAMRGSIDSLLALGEAIPPADRRELLESTRDEAERLDRYIQNLLDMTRLGHGGLKLARDWVAPGDIVGSALNRLRAVLAPYRVQAIVANDLPLLYVHAALIEQALINVLENAARFSPNHGRLRIEVSQDAAELRFAVSDEGPGIPEAEREKIFDMFYTAARGDRGGQGTGLGLAICQGMIGAHGGRISVGEGLDGRGTTLVLHLPLHPQPDLGQLEGDE

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0000155 Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
  • GO:0000160 A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
  • GO:0004673 Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
  • GO:0016772 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
  • GO:0016310 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Sequence Features

Domain/signature hits from InterPro and related databases.

60 records
Show feature table
Start End DB Term Name
2 876 PANTHER PTHR45569 SENSOR PROTEIN KDPD
390 408 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
501 644 Gene3D G3DSA:3.30.450.40 -
501 644 InterPro IPR029016 GAF-like domain superfamily
767 870 CDD cd00075 HATPase
16 226 Gene3D G3DSA:3.40.50.300 -
16 226 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
248 358 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
762 874 SMART SM00387 HKATPase_4
762 874 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
651 718 Pfam PF00512 His Kinase A (phospho-acceptor) domain
651 718 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
767 873 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
767 873 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
466 484 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
418 446 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
722 876 FunFam G3DSA:3.30.565.10:FF:000042 Two-component sensor histidine kinase KdpD
390 411 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
466 484 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
423 445 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
657 874 ProSiteProfiles PS50109 Histidine kinase domain profile.
657 874 InterPro IPR005467 Histidine kinase domain
385 489 Gene3D G3DSA:1.20.120.620 Backbone structure of the membrane domain of e. Coli histidine kinase receptor kdpd,
385 489 InterPro IPR038318 KdpD, transmembrane domain superfamily
833 851 PRINTS PR00344 Bacterial sensor protein C-terminal signature
833 851 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
799 813 PRINTS PR00344 Bacterial sensor protein C-terminal signature
799 813 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
858 871 PRINTS PR00344 Bacterial sensor protein C-terminal signature
858 871 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
817 827 PRINTS PR00344 Bacterial sensor protein C-terminal signature
817 827 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
390 494 Pfam PF13493 Domain of unknown function (DUF4118)
390 494 InterPro IPR025201 Sensor protein KdpD, transmembrane domain
248 358 Pfam PF00582 Universal stress protein family
248 358 InterPro IPR006016 UspA
648 714 CDD cd00082 HisKA
648 714 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
485 885 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
495 637 SUPERFAMILY SSF55781 GAF domain-like
650 718 SMART SM00388 HisKA_10
650 718 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
16 226 FunFam G3DSA:3.40.50.300:FF:000483 Sensor histidine kinase KdpD
645 717 Gene3D G3DSA:1.10.287.130 -
1 389 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
248 365 CDD cd01987 USP_OKCHK
447 465 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
229 361 Gene3D G3DSA:3.40.50.620 HUPs
229 361 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
733 878 Gene3D G3DSA:3.30.565.10 -
733 878 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
412 417 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
646 719 SUPERFAMILY SSF47384 Homodimeric domain of signal transducing histidine kinase
646 719 InterPro IPR036097 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily
692 712 Coils Coil Coil
645 717 FunFam G3DSA:1.10.287.130:FF:000027 Sensor histidine kinase KdpD
708 876 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
708 876 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
19 227 Pfam PF02702 Osmosensitive K+ channel His kinase sensor domain
19 227 InterPro IPR003852 Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1636
AlphaFold full sequence Viewing
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
1 0.536
2 0.249
5 0.204

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.

54 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
ANP P0AE82 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
EMC Q9X180 229.7 Da LogP 0.97 TPSA 0.0 ✓ Ro5 ✓ Clean CC[Hg+]
EMT Q9X180 382.8 Da LogP 2.91 TPSA 37.3 ✓ Ro5 ✓ Clean CC[Hg]Sc1ccccc1C(=O)O
PG0 P71815 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO

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.