Structure of PDB 5oef Chain A Binding Site BS01

Receptor Information
>5oef Chain A (length=574) Species: 1501 (Clostridium pasteurianum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICT
VEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGP
CNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLC
GRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIAC
PVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVT
GKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCC
PGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTV
TVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLED
SEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRG
LNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACH
GGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVK
MYQNYFGKPGEGRAHEILHFKYKK
Ligand information
Ligand ID9SQ
InChIInChI=1S/C2H7NSe2.2CN.3CO.2Fe/c4-1-3-2-5;5*1-2;;/h3-5H,1-2H2;;;;;;;/q;;;;2*+1;;
InChIKeyPHBGCQLNCRESHS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1NC[Se]2[Fe]3([Se]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]
CACTVS 3.385O=C1[Fe]([Se]CNC[Se][Fe]1(C#N)C#[O+])(C#N)C#[O+]
FormulaC7 H5 Fe2 N3 O3 Se2
Namedicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
ChEMBL
DrugBank
ZINC
PDB chain5oef Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5oef Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		A230 P231 S232 C299 P324 Q325 M353 P354 K358 F417 M497 C503
Binding residue
(residue number reindexed from 1)		A230 P231 S232 C299 P324 Q325 M353 P354 K358 F417 M497 C503
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E279 E282 C299 S319 K358 E361 Q366 C503
Catalytic site (residue number reindexed from 1) E279 E282 C299 S319 K358 E361 Q366 C503
Enzyme Commision number 1.12.7.2: ferredoxin hydrogenase.
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

View graph for
Molecular Function
External links
PDB RCSB:5oef, PDBe:5oef, PDBj:5oef
PDBsum5oef
PubMed29177350
UniProtP29166|PHF1_CLOPA Iron hydrogenase 1

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