Structure of PDB 8cm5 Chain A

Receptor sequence

>8cm5A (length=974) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough)

ELQKLQWAKQTTSICCYCAVGCGLIVHTAKDGQGRAVNVEGDPDHPINEG
SLCPKGASIFQLGENDQRGTQPLYRAPFSDTWKPVTWDFALTEIAKRIKK
TRDASFTEKNAAGDLVNRTEAIASFGSAAMDNEECWAYGNILRSLGLVYI
EHQARICHSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPI
AFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKY
ILDNKLYFTDYVREYTNASLIVGEKFSFKDGLFSGYDAANKKYDKSMWAF
ELDANGVPKRDPALKHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQV
YKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGNIGVAGG
GVNALRGESNVQGSTDQGLLAHIWPGYNPVPNSKAATLELYNAATPQSKD
PMSVNWWQNRPKYVASYLKALYPDEEPAAAYDYLPRIDAGRKLTDYFWLN
IFEKMDKGEFKGLFAWGMNPACGGANANKNRKAMGKLEWLVNVNLFENET
SSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGSVANSGRWMQWRYRGPKPY
AETKPDGDIMLDMFKKVRELYAKEGGAYPAPIAKLNIADWEEHNEFSPTK
VAKLMNGYFLKDTEVGGKQFKKGQQVPSFAFLTADGSTCSGNWLHAGSFT
DAGNLMARRDKTQTPEQARIGLFPNWSFCWPVNRRILYNRASVDKTGKPW
NPAKAVIEWKDGKWVGDVVDGGGDPGTKHPFIMQTHGFGALYGPGREEGP
FPEHYEPLECPVSKNPFSKQLHNPVAFQIEGEKKAVADPRYPFIGTTYRV
TEHWQTGLMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRG
ALEAVAIVTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSA
GDPNTGIPETKAFMVDVRKVWSHP

3D structure

• PDB: 8cm5 W-formate dehydrogenase C872A from Desulfovibrio vulgaris - with Formamide
• Chain: A
• Resolution: 2.15 Å

Enzymatic activity

• Enzyme Commision number: 1.2.1.2: Transferred entry: 1.17.1.9.

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	MGD	A	K90 G226 S227 N228 N232 D254 P255 R256 S272 D275 A404 M405 G406 H410 G442 E443 T881 Y883 R884 V885 T886 H888 W889 Q890 K996	K55 G191 S192 N193 N197 D219 P220 R221 S237 D240 A369 M370 G371 H375 G407 E408 T846 Y848 R849 V850 T851 H853 W854 Q855 K961
BS02	MGD	A	A164 Q188 I191 U192 Q409 E443 G552 M553 N554 G558 N579 L580 C608 D641 T882 R884 Q890 T891 L893 M894 W964 N979 T995	A129 Q153 I156 U157 Q374 E408 G517 M518 N519 G523 N544 L545 C573 D606 T847 R849 Q855 T856 L858 M859 W929 N944 T960
BS03	SF4	A	C50 C53 C57 L87 C88 I235	C15 C18 C22 L52 C53 I200

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0047111 formate dehydrogenase (cytochrome-c-553) activity
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0009061 anaerobic respiration
• GO:0045333 cellular respiration

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:8cm5, PDBe:8cm5, PDBj:8cm5
• PDBsum: 8cm5
• PubMed: 37985883
• UniProt: Q72EJ1