Protein profile

KP13_04718

Nitrite reductase [NAD(P)H] large subunit

Genome: KpKP13

Gene: AHE44017.1 Structure source: ColabFold UniProt A0A2V3K3L0
Amino acids 1355
Annotations 13
Features 73
PDB binders 4
Druggability 0.948

Overview

Basic information about this protein and its source genome.

Accession
KP13_04718
Gene
AHE44017.1
Status
annotated
Amino acids
1355
Structure source
ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.689
Human E-value
1.41e-16
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
89.5

Selected Druggability evidence

ColabFold / curated 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 0.948
Structure CB_KP13_04718
Pocket Pocket 90
P2Rank 0.884
Structure CB_KP13_04718
Pocket Pocket 1
ColabFold model
FPocket 0.948 · Pocket 90
P2Rank 0.884 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 50 / 4744 genomes with a hit
Normalized 0.011

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: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:0008860 Catalysis of the reaction: 2 reduced [2Fe-2S]-[ferredoxin] + NAD+ + H+ = 2 oxidized [2Fe-2S]-[ferredoxin] + NADH.
  • GO:0046872 Binding to a metal ion.
  • 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.

73 records
Show feature table
Start End DB Term Name
2 183 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
2 183 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1027 1191 Gene3D G3DSA:3.30.413.10 Sulfite Reductase Hemoprotein, domain 1
1027 1191 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
6 296 Gene3D G3DSA:3.50.50.60 -
6 296 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
820 867 Pfam PF04324 BFD-like [2Fe-2S] binding domain
820 867 InterPro IPR007419 BFD-like [2Fe-2S]-binding domain
508 642 Gene3D G3DSA:3.50.50.60 -
508 642 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1243 1343 ProSiteProfiles PS51296 Rieske [2Fe-2S] iron-sulfur domain profile.
1243 1343 InterPro IPR017941 Rieske [2Fe-2S] iron-sulphur domain
1239 1347 Gene3D G3DSA:2.102.10.10 -
1239 1347 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
1075 1093 PRINTS PR00397 Sirohaem Fe-binding site signature
1075 1093 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
1032 1050 PRINTS PR00397 Sirohaem Fe-binding site signature
1032 1050 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
956 1018 Pfam PF03460 Nitrite/Sulfite reductase ferredoxin-like half domain
956 1018 InterPro IPR005117 Nitrite/Sulfite reductase ferredoxin-like domain
308 382 Gene3D G3DSA:3.30.390.30 -
308 382 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
716 794 Gene3D G3DSA:3.30.390.30 -
716 794 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
113 230 Gene3D G3DSA:3.50.50.60 -
113 230 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1240 1345 ProSiteProfiles PS51300 NADH-nitrite reductase subunit D family profile.
3 372 PANTHER PTHR43809 NITRITE REDUCTASE (NADH) LARGE SUBUNIT
547 706 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
547 706 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1075 1091 ProSitePatterns PS00365 Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.
1075 1091 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
4 273 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
4 273 InterPro IPR023753 FAD/NAD(P)-binding domain
716 797 FunFam G3DSA:3.30.390.30:FF:000006 Nitrite reductase large subunit
404 685 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
404 685 InterPro IPR023753 FAD/NAD(P)-binding domain
404 1197 NCBIfam TIGR02374 nitrite reductase large subunit NirB
404 1197 InterPro IPR012744 Nitrite reductase [NAD(P)H] large subunit, NirB
405 679 Gene3D G3DSA:3.50.50.60 -
405 679 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
879 928 CDD cd19944 NirB_Fer2_BFD-like_2
309 374 Pfam PF18267 Rubredoxin NAD+ reductase C-terminal domain
309 374 InterPro IPR041575 NADH-rubredoxin oxidoreductase, C-terminal
716 785 Pfam PF18267 Rubredoxin NAD+ reductase C-terminal domain
716 785 InterPro IPR041575 NADH-rubredoxin oxidoreductase, C-terminal
1029 1201 SUPERFAMILY SSF56014 Nitrite and sulphite reductase 4Fe-4S domain-like
1029 1201 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
508 642 FunFam G3DSA:3.50.50.60:FF:000033 Nitrite reductase [NAD(P)H], large subunit
1243 1343 Pfam PF13806 Rieske-like [2Fe-2S] domain
1243 1343 InterPro IPR012748 Rieske-like [2Fe-2S] domain, NirD-type
399 588 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
399 588 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
898 1037 SUPERFAMILY SSF55124 Nitrite/Sulfite reductase N-terminal domain-like
898 1037 InterPro IPR036136 Nitrite/Sulfite reductase ferredoxin-like domain superfamily
1028 1166 Pfam PF01077 Nitrite and sulphite reductase 4Fe-4S domain
1028 1166 InterPro IPR006067 Nitrite/sulphite reductase 4Fe-4S domain
1243 1344 NCBIfam TIGR02378 nitrite reductase small subunit NirD
1243 1344 InterPro IPR012748 Rieske-like [2Fe-2S] domain, NirD-type
1243 1344 CDD cd03529 Rieske_NirD
1242 1345 SUPERFAMILY SSF50022 ISP domain
1242 1345 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
143 297 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
143 297 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
819 872 Gene3D G3DSA:1.10.10.1100 -
819 872 InterPro IPR041854 BFD-like [2Fe-2S]-binding domain superfamily
819 871 FunFam G3DSA:1.10.10.1100:FF:000002 Nitrite reductase large subunit
223 239 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
5 24 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
142 160 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
248 270 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
100 118 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
1034 1157 FunFam G3DSA:3.30.413.10:FF:000007 Nitrite reductase [NAD(P)H] large subunit

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 + 1

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

Entry Method Resolution Chain Coverage Links Status
ColabFold KP13_04718
ColabFold 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
90 0.948
1 0.297

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 11.39 0.609
2 9.61 0.517
3 8.54 0.456
4 8.14 0.433
5 8.14 0.433

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
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.