Protein profile

KP13_03298

Sensor protein kdpD

Genome: KpKP13

Gene: AHE45677.1 kdpD Structure source: AlphaFold + ColabFold UniProt A0A0H3GK10
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Amino acids 895
Annotations 13
Features 63
PDB binders 4
Druggability 0.334

Overview

Basic information about this protein and its source genome.

Accession
KP13_03298
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45677.1 kdpD
Status
annotated
Amino acids
895
Structure source
AlphaFold + ColabFold
EC
2.7.13.3
GO
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. GO:0016772 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GO:0004673 Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0005515 Binding to a protein. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
81.57

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 0.334
Structure A0A0H3GK10
Pocket Pocket 69
P2Rank 0.926
Structure A0A0H3GK10
Pocket Pocket 1
ColabFold model
FPocket 0.916 · Pocket 62
P2Rank 0.941 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 103 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • 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.
  • GO:0016772 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
  • GO:0004673 Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005515 Binding to a protein.
  • 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: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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

63 records
Show feature table
Start End DB Term Name
779 880 CDD cd00075 HATPase
512 656 FunFam G3DSA:3.30.450.40:FF:000038 Two-component sensor histidine kinase KdpD
1 398 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
253 365 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
253 373 CDD cd01987 USP_OKCHK
719 886 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
719 886 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
428 445 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
661 726 CDD cd00082 HisKA
661 726 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
448 465 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
19 229 Gene3D G3DSA:3.40.50.300 -
19 229 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
21 230 Pfam PF02702 Osmosensitive K+ channel His kinase sensor domain
21 230 InterPro IPR003852 Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal
501 895 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
466 476 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
829 839 PRINTS PR00344 Bacterial sensor protein C-terminal signature
829 839 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
868 881 PRINTS PR00344 Bacterial sensor protein C-terminal signature
868 881 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
844 862 PRINTS PR00344 Bacterial sensor protein C-terminal signature
844 862 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
811 825 PRINTS PR00344 Bacterial sensor protein C-terminal signature
811 825 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
19 229 FunFam G3DSA:3.40.50.300:FF:000483 Sensor histidine kinase KdpD
477 500 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
403 507 Pfam PF13493 Domain of unknown function (DUF4118)
403 507 InterPro IPR025201 Sensor protein KdpD, transmembrane domain
658 731 SUPERFAMILY SSF47384 Homodimeric domain of signal transducing histidine kinase
658 731 InterPro IPR036097 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily
734 886 FunFam G3DSA:3.30.565.10:FF:000042 Two-component sensor histidine kinase KdpD
658 732 Gene3D G3DSA:1.10.287.130 -
232 372 Gene3D G3DSA:3.40.50.620 HUPs
232 372 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
444 447 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
399 419 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 885 PANTHER PTHR45569 SENSOR PROTEIN KDPD
670 884 ProSiteProfiles PS50109 Histidine kinase domain profile.
670 884 InterPro IPR005467 Histidine kinase domain
665 730 Pfam PF00512 His Kinase A (phospho-acceptor) domain
665 730 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
774 884 SMART SM00387 HKATPase_4
774 884 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
733 883 Gene3D G3DSA:3.30.565.10 -
733 883 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
529 644 Pfam PF13492 GAF domain
529 644 InterPro IPR003018 GAF domain
401 423 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
420 424 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
396 502 Gene3D G3DSA:1.20.120.620 Backbone structure of the membrane domain of e. Coli histidine kinase receptor kdpd,
396 502 InterPro IPR038318 KdpD, transmembrane domain superfamily
512 657 Gene3D G3DSA:3.30.450.40 -
512 657 InterPro IPR029016 GAF-like domain superfamily
449 471 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
778 883 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
778 883 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
425 443 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
397 502 FunFam G3DSA:1.20.120.620:FF:000001 Two-component sensor histidine kinase KdpD
478 500 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
663 730 SMART SM00388 HisKA_10
663 730 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
239 372 FunFam G3DSA:3.40.50.620:FF:000169 Two-component system sensor histidine kinase KdbD

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_A0A0H3GK10
AlphaFold — — full sequence — Viewing
ColabFold KP13_03298
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
69 0.334
51 0.289
80 0.275

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 22.07 0.877
2 8.89 0.476
3 8.61 0.46
4 8.11 0.431

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
4BIW
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
3A0W
Q9X180 229.7 Da LogP 0.97 TPSA 0.0 ✓ Ro5 ✓ Clean CC[Hg+]
EMT
3A0W
Q9X180 382.8 Da LogP 2.91 TPSA 37.3 ✓ Ro5 ✓ Clean CC[Hg]Sc1ccccc1C(=O)O
RDC
3CGY
P0DM80 364.8 Da LogP 2.69 TPSA 96.4 ✓ Ro5 ✓ Clean C[C@@H]1C[C@@H]2[C@H](O2)\C=C/C=C/C(=O)Cc3c(c(c…

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.