Protein profile

KP13_32232

Formate dehydrogenase, nitrate-inducible, major subunit

Genome: KpKP13

Gene: AHE44401.1 fdnG Structure source: ColabFold UniProt A0A844PNL7
Amino acids 1025
Annotations 13
Features 40
PDB binders 12
Druggability 0.928

Overview

Basic information about this protein and its source genome.

Accession
KP13_32232
Gene
AHE44401.1 fdnG
Status
annotated
Amino acids
1025
Structure source
ColabFold

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
Periplasmic
ColabFold pLDDT
93.9

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 0.928
Structure CB_KP13_32232
Pocket Pocket 1
P2Rank 0.951
Structure CB_KP13_32232
Pocket Pocket 1
ColabFold model
FPocket 0.928 · Pocket 1
P2Rank 0.951 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 144 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

13 GO

Gene Ontology (GO)

13
  • GO:0047111 Catalysis of the reaction: ferricytochrome C-553 + formate = ferrocytochrome C-553 + CO2.
  • 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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
  • 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:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
  • GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
  • GO:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2).
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0036397 Catalysis of the reaction: formate + a quinone = CO2 + a quinol.
  • GO:0030151 Binding to a molybdenum ion (Mo).
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
  • GO:0015944 The chemical reactions and pathways by which formate is converted to CO2.

Sequence Features

Domain/signature hits from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
202 495 FunFam G3DSA:3.40.228.10:FF:000006 Formate dehydrogenase, alpha subunit, selenocysteine-containing
35 43 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
44 1025 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
54 114 Pfam PF04879 Molybdopterin oxidoreductase Fe4S4 domain
54 114 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
709 849 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
539 692 Gene3D G3DSA:3.40.50.740 -
1 43 ProSiteProfiles PS51318 Twin arginine translocation (Tat) signal profile.
1 43 InterPro IPR006311 Twin-arginine translocation pathway, signal sequence
45 169 FunFam G3DSA:3.30.200.210:FF:000003 Formate dehydrogenase-N subunit alpha
11 1025 PANTHER PTHR43598 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE 2 SUBUNIT B
863 1025 SUPERFAMILY SSF50692 ADC-like
863 1025 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
850 1025 Gene3D G3DSA:2.40.40.20 -
21 34 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
903 1018 Pfam PF01568 Molydopterin dinucleotide binding domain
903 1018 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
45 168 Gene3D G3DSA:3.30.200.210 -
527 692 FunFam G3DSA:3.40.50.740:FF:000007 Formate dehydrogenase, alpha subunit, selenocysteine-containing
117 599 Pfam PF00384 Molybdopterin oxidoreductase
117 599 InterPro IPR006656 Molybdopterin oxidoreductase
53 116 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
53 116 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
1 20 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 43 Phobius SIGNAL_PEPTIDE Signal peptide region
896 1024 CDD cd02792 MopB_CT_Formate-Dh-Na-like
46 860 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
53 114 SMART SM00926 Molybdop_Fe4S4_2
53 114 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
850 1025 FunFam G3DSA:2.40.40.20:FF:000017 Formate dehydrogenase, alpha subunit
202 492 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
57 883 CDD cd02752 MopB_Formate-Dh-Na-like
12 1024 NCBIfam TIGR01553 formate dehydrogenase-N subunit alpha
12 1024 InterPro IPR006443 Formate dehydrogenase-N, alpha subunit
701 849 FunFam G3DSA:3.40.228.10:FF:000011 Formate dehydrogenase-N subunit alpha
937 964 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
937 964 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
58 76 ProSitePatterns PS00551 Prokaryotic molybdopterin oxidoreductases signature 1.
58 76 InterPro IPR027467 Molybdopterin oxidoreductase, molybdopterin cofactor binding site

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_32232
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
1 0.928
23 0.358
2 0.214

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 24.67 0.9
2 10.98 0.589
3 7.35 0.384
4 7.14 0.371
5 5.16 0.238

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.

62 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
2MD Q934F5 742.6 Da LogP -2.53 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
4MO P07658 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+4]
6MO P24183 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
CDL P24183 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
FES D5AQH0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
H2S Q72EJ1 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
HQO P24183 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
LCP P81186 99.4 Da LogP -4.76 TPSA 92.2 ✓ Ro5 ✓ Clean [O-]Cl(=O)(=O)=O
MGD P24183 740.6 Da LogP -2.06 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
MO P81186 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
NO2 P81186 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]
W Q72EJ1 183.8 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [W+6]

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.