Structure of PDB 1fdo Chain A

Receptor sequence

>1fdoA (length=715) Species: 562 (Escherichia coli)

MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWD
FINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGP
DAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVCHGPSVAGLHQ
SVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIV
CDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTE
GFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVT
QFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDT
YPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYI
MGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGE
HEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQE
IWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDT
PNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAA
LADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAI
YMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVID
EYNKLKTRLREAALA

3D structure

• PDB: 1fdo Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.
• Chain: A
• Resolution: 2.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C11 L41 C42 K44 S108 R110 D134 C140 H141 S180 M297 R333 G334 Q335
• Catalytic site (residue number reindexed from 1): C11 L41 C42 K44 S108 R110 D134 C140 H141 S180 M297 R333 G334 Q335
• Enzyme Commision number: 1.17.98.4: formate dehydrogenase (acceptor).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SF4	A	C8 Y10 C11 S13 C15 C42 K44 G45 P182 I183	C8 Y10 C11 S13 C15 C42 K44 G45 P182 I183
BS02	MGD	A	R110 V139 U140 Q301 Q335 G402 E403 T408 Q428 D429 I430 S445 D478 T579 R581 C588 Y654 N662 Y678	R110 V139 U140 Q301 Q335 G402 E403 T408 Q428 D429 I430 S445 D478 T579 R581 C588 Y654 N662 Y678
BS03	MGD	A	K44 F173 G174 Y175 N176 D179 S180 D202 P203 R204 L218 G221 N223 M297 G298 F302 G334 Q335 V580 R581 E582 H585 Y586 S587 K679	K44 F173 G174 Y175 N176 D179 S180 D202 P203 R204 L218 G221 N223 M297 G298 F302 G334 Q335 V580 R581 E582 H585 Y586 S587 K679

Gene Ontology

Molecular Function

• GO:0003954 NADH dehydrogenase activity
• GO:0005515 protein binding
• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006007 glucose catabolic process
• GO:0009061 anaerobic respiration
• GO:0015942 formate metabolic process
• GO:0015944 formate oxidation
• GO:0019628 urate catabolic process
• GO:0019645 anaerobic electron transport chain
• GO:0045333 cellular respiration

Cellular Component

• GO:0005829 cytosol
• GO:0009326 formate dehydrogenase complex
• GO:0016020 membrane
• GO:0045271 respiratory chain complex I
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:1fdo, PDBe:1fdo, PDBj:1fdo
• PDBsum: 1fdo
• PubMed: 9036855
• UniProt: P07658|FDHF_ECOLI Formate dehydrogenase H (Gene Name=fdhF)