1kqf Summary

pdbe.org/1kqf
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FORMATE DEHYDROGENASE N FROM E. COLI

The structure was published by Jormakka, M., Tornroth, S., Byrne, B., and Iwata, S., in 2002 in a paper entitled "Molecular basis of proton motive force generation: structure of formate dehydrogenase-N." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.6 Å and deposited in 2002.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT, FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT, and FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterononamer.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT P24183 (1-1015) (FDNG_ECOLI)search Escherichia coli K-12search < 90% 1015 96%
B FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT P0AAJ3 (1-294) (FDNH_ECOLI)search Escherichia coli K-12search 100% 294 98%
C FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT P0AEK7 (1-217) (FDNI_ECOLI)search Escherichia coli K-12search 100% 217 99%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
P24183 (1 - 1015) FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT Escherichia coli
P0AAJ3 (1 - 294) FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT Escherichia coli
P0AEK7 (1 - 217) FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT Escherichia coli

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A Formate dehydrogenase/DMSO reductase, C-terminal domainsearch, Formate dehydrogenase/DMSO reductase, domains 1-3search Rossmann foldsearch, Dimethylsulfoxide Reductase, domain 2search, Barwin-like endoglucanasessearch Molybdopterin oxidoreductasesearch, Molydopterin dinucleotide binding domainsearch, Molybdopterin oxidoreductase Fe4S4 domainsearch
B (P0AAJ3) Ferredoxin domains from multidomain proteinssearch, Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchorsearch Alpha-Beta Plaitssearch, Single helix binsearch PF09163: Formate dehydrogenase N, transmembranesearch, PF13247: 4Fe-4S dicluster domainsearch
C (P0AEK7) Formate dehydrogenase N, cytochrome (gamma) subunitsearch Transmembrane di-heme cytochromes, Chain Csearch PF00033: Cytochrome b(N-terminal)/b6/petBsearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A (P24183) oxidation-reduction processsearch cellular respirationsearch formate dehydrogenase (NAD+) activitysearch oxidoreductase activitysearch 4 iron, 4 sulfur cluster bindingsearch molybdenum ion bindingsearch electron carrier activitysearch cytoplasmsearch
B (P0AAJ3) cellular respirationsearch oxidation-reduction processsearch anaerobic respirationsearch iron-sulfur cluster bindingsearch formate dehydrogenase (NAD+) activitysearch 4 iron, 4 sulfur cluster bindingsearch metal ion bindingsearch integral component of membranesearch membranesearch plasma membranesearch formate dehydrogenase complexsearch
C (P0AEK7) cellular respirationsearch respiratory electron transport chainsearch anaerobic respirationsearch cytochrome complex assemblysearch oxidation-reduction processsearch formate dehydrogenase (NAD+) activitysearch metal ion bindingsearch electron carrier activitysearch integral component of membranesearch formate dehydrogenase complexsearch membranesearch plasma membranesearch

Chain InterPro annotation
A Twin-arginine translocation pathway, signal sequencesearch Formate dehydrogenase, alpha subunit, anaerobicsearch Molybdopterin oxidoreductase, prokaryotic, conserved sitesearch Molybdopterin oxidoreductasesearch Molydopterin dinucleotide-binding domainsearch Molybdopterin oxidoreductase, 4Fe-4S domainsearch Aspartate decarboxylase-like domainsearch Molybdopterin oxidoreductase, molybdopterin cofactor binding sitesearch
B 4Fe-4S binding domainsearch Formate dehydrogenase, beta subunitsearch Formate dehydrogenase, iron-sulphur subunitsearch Formate dehydrogenase, transmembranesearch 4Fe-4S ferredoxin-type, iron-sulphur binding domainsearch 4Fe-4S ferredoxin, iron-sulphur binding, conserved sitesearch
C Formate dehydrogenase, gamma subunitsearch Di-haem cytochrome, transmembranesearch