Structure of PDB 5d0a Chain B Binding Site BS03

Receptor Information
>5d0a Chain B (length=379) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEE
PDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASW
GKDYHDVLREKLDLLEDFLKSKHDIRTKSMVDTGELSDRAVAERAGIGFS
AKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGA
LVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKG
KDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQR
NAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEEL
EKALEKEKDEEAKLEIEKGIELLKASGMT
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain5d0a Chain B Residue 502 [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]
PDB5d0a Molecular basis of cobalamin-dependent RNA modification.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		C198 P199 C214 I215 C240 C243
Binding residue
(residue number reindexed from 1)		C196 P197 C212 I213 C238 C241
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.99.6: epoxyqueuosine reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0052693 epoxyqueuosine reductase activity
Biological Process
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0008616 queuosine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5d0a, PDBe:5d0a, PDBj:5d0a
PDBsum5d0a
PubMed27638883
UniProtP97030|QUEG_BACSU Epoxyqueuosine reductase (Gene Name=queG)

[Back to BioLiP]