Structure of PDB 5bys Chain B

Receptor sequence

>5bysB (length=571) Species: 1501 (Clostridium pasteurianum)

KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTV
EVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPC
NRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCG
RCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACP
VAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTG
KIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCP
GWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVT
VMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDS
EADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGL
NGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHG
GCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKM
YQNYFGKPGEGRAHEILHFKY

3D structure

• PDB: 5bys A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.
• Chain: B
• Resolution: 1.93 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E279 E282 C299 S319 K358 E361 Q366 C503
• Catalytic site (residue number reindexed from 1): E278 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	SF4	B	C300 C355 M497 A498 C499 C503	C299 C354 M496 A497 C498 C502
BS02	SF4	B	C157 T161 A165 M166 C190 L191 L192 C193 G194 Q195 C196	C156 T160 A164 M165 C189 L190 L191 C192 G193 Q194 C195
BS03	SF4	B	C147 L148 L149 C150 G151 C153 I177 C200 P201 A204 L205	C146 L147 L148 C149 G150 C152 I176 C199 P200 A203 L204
BS04	SF4	B	H94 F96 K97 C98 C101 R104 C107 V202	H93 F95 K96 C97 C100 R103 C106 V201
BS05	FES	B	A32 C34 F35 C46 E47 C49 C62	A31 C33 F34 C45 E46 C48 C61
BS06	4WX	B	A230 P231 S232 I268 C299 P324 Q325 M353 P354 K358 F417 V423 M497 C503	A229 P230 S231 I267 C298 P323 Q324 M352 P353 K357 F416 V422 M496 C502
BS07	MG	B	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:5bys, PDBe:5bys, PDBj:5bys
• PDBsum: 5bys
• PubMed: 29896366
• UniProt: P29166|PHF1_CLOPA Iron hydrogenase 1