Protein profile

KP13_04529

Formate dehydrogenase, nitrate-inducible, cytochrome b556(fdn) subunit

Genome: KpKP13

Gene: AHE44404.1 fdnI Structure source: AlphaFold + ColabFold UniProt A0A0H3GTC9
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Amino acids 213
Annotations 11
Features 22
PDB binders 4
Druggability 0.988

Overview

Basic information about this protein and its source genome.

Accession
KP13_04529
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44404.1 fdnI
Status
annotated
Amino acids
213
Structure source
AlphaFold + ColabFold
GO
GO:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH. 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. GO:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2). 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).

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
CytoplasmicMembrane
ColabFold pLDDT
96.06

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 0.988
Structure A0A0H3GTC9
Pocket Pocket 15
P2Rank 0.995
Structure A0A0H3GTC9
Pocket Pocket 1
ColabFold model
FPocket 0.987 · Pocket 11
P2Rank 0.993 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 117 / 4744 genomes with a hit
Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
  • GO:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2).
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0036397 Catalysis of the reaction: formate + a quinone = CO2 + a quinol.
  • GO:0046872 Binding to a metal ion.
  • 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.

22 records
Show feature table
Start End DB Term Name
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 207 PANTHER PTHR30074 FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556 FDN SUBUNIT
72 109 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
170 213 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
149 171 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
131 141 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
50 71 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
50 72 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
39 49 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 209 FunFam G3DSA:1.20.950.20:FF:000002 Formate dehydrogenase cytochrome b556 subunit
7 181 Pfam PF01292 Prokaryotic cytochrome b561
7 181 InterPro IPR011577 Cytochrome b561, bacterial/Ni-hydrogenase
142 169 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
110 130 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 212 Gene3D G3DSA:1.20.950.20 -
2 204 SUPERFAMILY SSF81342 Transmembrane di-heme cytochromes
2 204 InterPro IPR016174 Di-haem cytochrome, transmembrane
12 38 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
112 134 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 201 NCBIfam TIGR01583 formate dehydrogenase subunit gamma
2 201 InterPro IPR006471 Formate dehydrogenase, gamma 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 + 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_A0A0H3GTC9
AlphaFold — — full sequence — Viewing
ColabFold KP13_04529
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
15 0.988
3 0.945

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 63.73 0.989
2 29.77 0.932
3 1.78 0.033
4 1.09 0.007

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
6MO
1KQF
P0AEK7 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
CDL
1KQF
P0AEK7 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
HQO
1KQG
P0AEK7 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MGD
1KQF
P0AEK7 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@@](=…

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.