Protein profile

VK055_3717

nitrite reductase [NAD(P)H] small subunit

Genome: KpATCC43816

Gene: nirD2 AIK82272.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWR0
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Amino acids 108
Annotations 7
Features 14
PDB binders 0
Druggability 0.105

Overview

Basic information about this protein and its source genome.

Accession
VK055_3717
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
nirD2 AIK82272.1
Status
annotated
Amino acids
108
Structure source
AlphaFold + ColabFold
EC
1.7.1.15
GO
GO:0008942 Catalysis of the reaction: NH4+ + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H + 5 H+. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0009344 Complex that possesses nitrite reductase [NAD(P)H] activity. GO:0106316 Catalysis of the reaction: NH4+ + 3 NAD+ + 2 H2O = nitrite + 3 NADH + 5 H+. GO:0042128 The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.

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
Cytoplasmic
ColabFold pLDDT
96.59

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 0.105
Structure A0A0H3GWR0
Pocket Pocket 2
P2Rank
Structure A0A0H3GWR0
Pocket No pockets
ColabFold model
FPocket 0.172 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 109 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0008942 Catalysis of the reaction: NH4+ + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H + 5 H+.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009344 Complex that possesses nitrite reductase [NAD(P)H] activity.
  • GO:0106316 Catalysis of the reaction: NH4+ + 3 NAD+ + 2 H2O = nitrite + 3 NADH + 5 H+.
  • GO:0042128 The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
2 107 PANTHER PTHR40562 -
2 107 InterPro IPR017881 Nitrite reductase (NADH) small subunit
1 108 Gene3D G3DSA:2.102.10.10 -
1 108 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
3 106 Pfam PF13806 Rieske-like [2Fe-2S] domain
3 106 InterPro IPR012748 Rieske-like [2Fe-2S] domain, NirD-type
1 108 ProSiteProfiles PS51300 NADH-nitrite reductase subunit D family profile.
1 107 SUPERFAMILY SSF50022 ISP domain
1 107 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
4 107 CDD cd03529 Rieske_NirD
4 107 InterPro IPR012748 Rieske-like [2Fe-2S] domain, NirD-type
1 108 FunFam G3DSA:2.102.10.10:FF:000002 Nitrite reductase [NAD(P)H] small subunit
3 107 NCBIfam TIGR02378 nitrite reductase small subunit NirD
3 107 InterPro IPR012748 Rieske-like [2Fe-2S] domain, NirD-type

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

No pockets are loaded yet for the displayed AlphaFold model AF_A0A0H3GWR0 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

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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_A0A0H3GWR0
AlphaFold — — full sequence — Viewing
ColabFold VK055_3717
ColabFold — — full sequence — Loaded