Protein profile

KP13_02922

Na(+)-translocating NADH-quinone reductase subunit D

Genome: KpKP13

Gene: nqrD AHE46198.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN35
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Amino acids 212
Annotations 6
Features 28
PDB binders 0
Druggability 0.807

Overview

Basic information about this protein and its source genome.

Accession
KP13_02922
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nqrD AHE46198.1
Status
annotated
Amino acids
212
Structure source
AlphaFold + ColabFold
EC
7.2.1.1
GO
GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0012505 A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. 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:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

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 (%)
74.519
DEG E-value
2.9599999999999997e-115
Localization
CytoplasmicMembrane
ColabFold pLDDT
84.38

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 0.807
Structure A0A0H3GN35
Pocket Pocket 5
P2Rank 0.026
Structure A0A0H3GN35
Pocket Pocket 1
ColabFold model
FPocket 0.771 · Pocket 4
P2Rank 0.019 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 614 / 4744 genomes with a hit
Normalized 0.129

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0012505 A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
  • 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:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
44 65 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
182 201 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
64 74 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
75 97 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 37 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 210 NCBIfam TIGR01939 NADH:ubiquinone reductase (Na(+)-transporting) subunit D
8 210 InterPro IPR011292 Na(+)-translocating NADH-quinone reductase subunit D
6 212 PIRSF PIRSF006102 NQR_DE
6 212 InterPro IPR003667 NqrDE/RnfAE
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 210 Hamap MF_00428 Na(+)-translocating NADH-quinone reductase subunit D [nqrD].
5 210 InterPro IPR011292 Na(+)-translocating NADH-quinone reductase subunit D
182 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
133 154 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 198 Pfam PF02508 Rnf-Nqr subunit, membrane protein
12 198 InterPro IPR003667 NqrDE/RnfAE
15 37 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
43 63 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 97 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
98 102 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 211 PANTHER PTHR30586 ELECTRON TRANSPORT COMPLEX PROTEIN RNFE
131 153 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
103 121 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
122 132 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
155 181 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
202 212 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
104 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GN35
AlphaFold — — full sequence — Viewing
ColabFold KP13_02922
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 0.807
2 0.294

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 1.13 0.009
2 1.08 0.007
3 1.04 0.006