Protein profile

KP13_00712

Nitrite reductase [NAD(P)H] large subunit

Genome: KpKP13

Gene: AHE42330.1 nirB Structure source: AlphaFold + ColabFold UniProt A0A0H3GYE4
Amino acids 847
Annotations 12
Features 57
PDB binders 4
Druggability 0.967

Overview

Basic information about this protein and its source genome.

Accession
KP13_00712
Gene
AHE42330.1 nirB
Status
annotated
Amino acids
847
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.615
Human E-value
3.68e-23
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
90.64

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 0.967
Structure A0A0H3GYE4
Pocket Pocket 20
P2Rank 0.819
Structure A0A0H3GYE4
Pocket Pocket 1
ColabFold model
FPocket 1 · Pocket 2
P2Rank 0.802 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 129 / 4744 genomes with a hit
Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

12 GO

Gene Ontology (GO)

12
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • 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.
  • GO:0008942 Catalysis of the reaction: NH4+ + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H + 5 H+.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • 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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0098809 Catalysis of the reaction: nitrite + acceptor = product(s) of nitrate reduction + reduced acceptor.
  • GO:0015980 The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.

Sequence Features

Domain/signature hits from InterPro and related databases.

57 records
Show feature table
Start End DB Term Name
423 475 FunFam G3DSA:1.10.10.1100:FF:000002 Nitrite reductase large subunit
638 761 FunFam G3DSA:3.30.413.10:FF:000007 Nitrite reductase [NAD(P)H] large subunit
769 789 Coils Coil Coil
423 476 Gene3D G3DSA:1.10.10.1100 -
423 476 InterPro IPR041854 BFD-like [2Fe-2S]-binding domain superfamily
8 283 Gene3D G3DSA:3.50.50.60 -
8 283 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
144 310 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
144 310 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
320 401 Gene3D G3DSA:3.30.390.30 -
320 401 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
110 246 Gene3D G3DSA:3.50.50.60 -
110 246 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
633 767 Pfam PF01077 Nitrite and sulphite reductase 4Fe-4S domain
633 767 InterPro IPR006067 Nitrite/sulphite reductase 4Fe-4S domain
261 283 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
102 120 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
6 25 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
147 165 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
234 250 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
110 246 FunFam G3DSA:3.50.50.60:FF:000033 Nitrite reductase [NAD(P)H], large subunit
639 761 Gene3D G3DSA:3.30.413.10 Sulfite Reductase Hemoprotein, domain 1
639 761 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
5 292 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
5 292 InterPro IPR023753 FAD/NAD(P)-binding domain
2 833 PANTHER PTHR43809 NITRITE REDUCTASE (NADH) LARGE SUBUNIT
424 471 Pfam PF04324 BFD-like [2Fe-2S] binding domain
424 471 InterPro IPR007419 BFD-like [2Fe-2S]-binding domain
545 638 FunFam G3DSA:3.90.480.20:FF:000001 Nitrite reductase [NAD(P)H] large subunit
320 401 FunFam G3DSA:3.30.390.30:FF:000006 Nitrite reductase large subunit
321 387 Pfam PF18267 Rubredoxin NAD+ reductase C-terminal domain
321 387 InterPro IPR041575 NADH-rubredoxin oxidoreductase, C-terminal
542 638 Gene3D G3DSA:3.90.480.20 -
633 808 SUPERFAMILY SSF56014 Nitrite and sulphite reductase 4Fe-4S domain-like
633 808 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
679 695 ProSitePatterns PS00365 Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.
679 695 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
560 622 Pfam PF03460 Nitrite/Sulfite reductase ferredoxin-like half domain
560 622 InterPro IPR005117 Nitrite/Sulfite reductase ferredoxin-like domain
679 697 PRINTS PR00397 Sirohaem Fe-binding site signature
679 697 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
636 654 PRINTS PR00397 Sirohaem Fe-binding site signature
636 654 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
6 801 NCBIfam TIGR02374 nitrite reductase large subunit NirB
6 801 InterPro IPR012744 Nitrite reductase [NAD(P)H] large subunit, NirB
2 189 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
2 189 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
483 532 CDD cd19944 NirB_Fer2_BFD-like_2
419 470 CDD cd19943 NirB_Fer2_BFD-like_1
1 835 PIRSF PIRSF037149 NirB
1 835 InterPro IPR017121 Nitrite reductase [NAD(P)H], large subunit
502 627 SUPERFAMILY SSF55124 Nitrite/Sulfite reductase N-terminal domain-like
502 627 InterPro IPR036136 Nitrite/Sulfite reductase ferredoxin-like domain superfamily
276 283 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
235 249 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
147 172 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
105 114 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature

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_A0A0H3GYE4
AlphaFold full sequence Viewing
ColabFold KP13_00712
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
20 0.967
23 0.373

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 13.88 0.702
2 11.27 0.603
3 6.01 0.296
4 3.0 0.098
5 1.94 0.04

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.

72 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
APR Q52437 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AZI Q5XC60 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
BU3 Q47QF8 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
OXY Q03Q85 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=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.