Protein profile

KP13_02008

Trifunctional NAD biosynthesis/regulator protein NadR

Genome: KpKP13

Gene: AHE46445.1 nadR Structure source: AlphaFold + ColabFold UniProt A0A0H3GM95
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Amino acids 410
Annotations 11
Features 34
PDB binders 0
Druggability 0.958

Overview

Basic information about this protein and its source genome.

Accession
KP13_02008
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46445.1 nadR
Status
annotated
Amino acids
410
Structure source
AlphaFold + ColabFold
EC
2.7.1.22 2.7.7.1
GO
GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3. GO:0000309 Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0050262 Catalysis of the reaction: beta-nicotinamide D-riboside + ATP = beta-nicotinamide D-ribonucleotide + ADP + H+. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 (%)
54.441
DEG E-value
9.78e-141
Localization
Cytoplasmic
ColabFold pLDDT
91.39

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 0.958
Structure A0A0H3GM95
Pocket Pocket 2
P2Rank 0.942
Structure A0A0H3GM95
Pocket Pocket 1
ColabFold model
FPocket 0.812 · Pocket 1
P2Rank 0.943 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 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.

2 EC 9 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

9
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
  • GO:0000309 Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0050262 Catalysis of the reaction: beta-nicotinamide D-riboside + ATP = beta-nicotinamide D-ribonucleotide + ADP + H+.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
2 410 PIRSF PIRSF004776 NadR_NMNAT/RNK
2 410 InterPro IPR016429 NAD biosynthesis/regulator protein NadR
63 230 Gene3D G3DSA:3.40.50.620 HUPs
63 230 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
232 386 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
232 386 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
5 60 FunFam G3DSA:1.10.260.40:FF:000020 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
7 62 ProSiteProfiles PS50943 Cro/C1-type HTH domain profile.
7 62 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
66 409 PANTHER PTHR37512 TRIFUNCTIONAL NAD BIOSYNTHESIS/REGULATOR PROTEIN NADR
64 395 NCBIfam TIGR01526 nicotinamide-nucleotide adenylyltransferase
64 395 InterPro IPR006417 Nicotinamide-nucleotide adenylyltransferase
7 59 CDD cd00093 HTH_XRE
7 59 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
6 62 SMART SM00530 mbf_short4
6 62 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
63 230 FunFam G3DSA:3.40.50.620:FF:000091 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
66 136 NCBIfam TIGR00125 cytidyltransferase-like domain
66 136 InterPro IPR004821 Cytidyltransferase-like domain
66 227 CDD cd02167 NMNAT_NadR
66 227 InterPro IPR041749 NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain
7 58 Pfam PF01381 Helix-turn-helix
7 58 InterPro IPR001387 Cro/C1-type helix-turn-helix domain
231 397 FunFam G3DSA:3.40.50.300:FF:000672 Trifunctional nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase/transcriptional regulator NadR
231 397 Gene3D G3DSA:3.40.50.300 -
231 397 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
6 60 SUPERFAMILY SSF47413 lambda repressor-like DNA-binding domains
6 60 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
66 229 SUPERFAMILY SSF52374 Nucleotidylyl transferase
233 260 CDD cd02019 NK
5 60 Gene3D G3DSA:1.10.260.40 -
5 60 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
234 394 Pfam PF13521 AAA domain
234 394 InterPro IPR038727 NadR/Ttd14, AAA domain

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_A0A0H3GM95
AlphaFold — — full sequence — Viewing
ColabFold KP13_02008
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
2 0.958
17 0.816
7 0.261

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 24.94 0.902
2 10.42 0.56
3 2.77 0.084
4 1.77 0.033