Structure of PDB 6yf4 Chain A

Receptor sequence

>6yf4A (length=580) Species: 1501 (Clostridium pasteurianum)

KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTV
EVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPC
NRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCG
RCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACP
VAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTG
KIYTALRQLGFDKIFDINFGADMTIMEDATELVQRIENNGPFPMFTSCCP
GWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVT
VMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDS
EADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGL
NGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHG
GCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKM
YQNYFGKPGEGRAHEILHFKYKKSAWSHPQ

3D structure

• PDB: 6yf4 The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases.
• Chain: A
• Resolution: 1.77 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D279 E282 C299 S319 K358 E361 Q366 C503
• Catalytic site (residue number reindexed from 1): D278 E281 C298 S318 K357 E360 Q365 C502
• Enzyme Commision number: 1.12.7.2: ferredoxin hydrogenase.

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	402	A	A230 P231 S232 C299 P324 Q325 M353 P354 K358 F417 M497 C503	A229 P230 S231 C298 P323 Q324 M352 P353 K357 F416 M496 C502
BS02	SF4	A	C300 C355 M497 A498 C499 C503	C299 C354 M496 A497 C498 C502
BS03	SF4	A	C157 T161 A165 M166 C190 L191 L192 C193 G194 C196	C156 T160 A164 M165 C189 L190 L191 C192 G193 C195
BS04	SF4	A	C147 L148 L149 C150 G151 C153 I177 C200 P201 A204 L205	C146 L147 L148 C149 G150 C152 I176 C199 P200 A203 L204
BS05	SF4	A	H94 F96 K97 C98 C101 R103 C107 V202	H93 F95 K96 C97 C100 R102 C106 V201
BS06	FES	A	A32 C34 F35 C46 E47 C49 C62	A31 C33 F34 C45 E46 C48 C61
BS07	MG	A	N40 D42	N39 D41

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0008901 ferredoxin hydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:6yf4, PDBe:6yf4, PDBj:6yf4
• PDBsum: 6yf4
• PubMed: 32796105
• UniProt: P29166|PHF1_CLOPA Iron hydrogenase 1