Structure of PDB 6gm3 Chain B Binding Site BS01

Receptor Information
>6gm3 Chain B (length=575) Species: 1501 (Clostridium pasteurianum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTV
EVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPC
NRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCG
RCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACP
VAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTG
KIYTALRQLGFDKIFDINFGADMTIMEEATELVQAIENNGPFPMFTSCCP
GWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVT
VMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDS
EADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGL
NGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHG
GCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKM
YQNYFGKPGEGRAHEILHFKYKKSA
Ligand information
Ligand ID402
InChIInChI=1S/C2H5NS2.2CN.3CO.2Fe/c4-1-3-2-5;5*1-2;;/h3H,1-2H2;;;;;;;/q;;;;2*+1;;
InChIKeyLJPDYWPSPOWMIB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2[Fe]1(C#N)(C#[O+])S3CNCS1[Fe]23(C#[O+])C#N
CACTVS 3.385O=C1[Fe](SCNCS[Fe]1(C#N)C#[O+])(C#N)C#[O+]
OpenEye OEToolkits 1.9.2C1NC[S]2[Fe]3([S]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]
FormulaC7 H5 Fe2 N3 O3 S2
Namedicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
ChEMBL
DrugBank
ZINC
PDB chain6gm3 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6gm3 Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		A230 P231 S232 I268 C299 P324 Q325 M353 P354 K358 F417 M497 C503
Binding residue
(residue number reindexed from 1)		A229 P230 S231 I267 C298 P323 Q324 M352 P353 K357 F416 M496 C502
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) E278 E281 C298 S318 K357 E360 Q365 C502
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:6gm3, PDBe:6gm3, PDBj:6gm3
PDBsum6gm3
PubMed30413719
UniProtP29166|PHF1_CLOPA Iron hydrogenase 1

[Back to BioLiP]