Protein profile

VK055_0617

formate dehydrogenase, alpha subunit

Genome: KpATCC43816

Gene: AIK79240.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYA2
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Amino acids 803
Annotations 10
Features 21
PDB binders 12
Druggability 0.991

Overview

Basic information about this protein and its source genome.

Accession
VK055_0617
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79240.1
Status
annotated
Amino acids
803
Structure source
AlphaFold + ColabFold
GO
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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH. 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: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: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:0047111 Catalysis of the reaction: ferricytochrome C-553 + formate = ferrocytochrome C-553 + CO2.

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 (%)
25.63
Localization
Periplasmic
ColabFold pLDDT
98.55

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 0.991
Structure A0A0H3GYA2
Pocket Pocket 2
P2Rank 0.928
Structure A0A0H3GYA2
Pocket Pocket 1
ColabFold model
FPocket 0.936 · Pocket 1
P2Rank 0.924 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 147 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • 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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
  • 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: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: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:0047111 Catalysis of the reaction: ferricytochrome C-553 + formate = ferrocytochrome C-553 + CO2.
  • GO:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 270 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
674 802 CDD cd02792 MopB_CT_Formate-Dh-Na-like
479 627 FunFam G3DSA:3.40.228.10:FF:000011 Formate dehydrogenase-N subunit alpha
715 742 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
715 742 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
483 627 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
628 803 Gene3D G3DSA:2.40.40.20 -
628 803 FunFam G3DSA:2.40.40.20:FF:000017 Formate dehydrogenase, alpha subunit
1 802 NCBIfam TIGR01553 formate dehydrogenase-N subunit alpha
1 802 InterPro IPR006443 Formate dehydrogenase-N, alpha subunit
2 377 Pfam PF00384 Molybdopterin oxidoreductase
2 377 InterPro IPR006656 Molybdopterin oxidoreductase
317 470 Gene3D G3DSA:3.40.50.740 -
641 803 SUPERFAMILY SSF50692 ADC-like
641 803 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
1 273 FunFam G3DSA:3.40.228.10:FF:000006 Formate dehydrogenase, alpha subunit, selenocysteine-containing
305 470 FunFam G3DSA:3.40.50.740:FF:000007 Formate dehydrogenase, alpha subunit, selenocysteine-containing
681 796 Pfam PF01568 Molydopterin dinucleotide binding domain
681 796 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
1 638 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
1 803 PANTHER PTHR43598 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE 2 SUBUNIT B

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_A0A0H3GYA2
AlphaFold — — full sequence — Viewing
ColabFold VK055_0617
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 0.991
1 0.89
5 0.87
39 0.414

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 17.67 0.806
2 15.9 0.765
3 10.92 0.586
4 8.6 0.46
5 7.47 0.392

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
2IV2
P07658 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
1AA6
P07658 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+4]
6MO
1KQF
P24183 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
CDL
1KQF
P24183 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
H2S
6SDV
Q72EJ1 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
HQO
1KQG
P24183 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
LCP
2V3V
P81186 99.4 Da LogP -4.76 TPSA 92.2 ✓ Ro5 ✓ Clean [O-]Cl(=O)(=O)=O
MGD
1KQF
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
2JIM
P81186 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
MOS
3ML1
P39185 161.0 Da LogP 0.14 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo](=O)S
NO2
2JIQ
P81186 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]
W
6SDV
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.