Structure of PDB 2y0f Chain D Binding Site BS01

Receptor Information
>2y0f Chain D (length=393) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGSE
IVRLTVNDEEAAKAVPEIKRRLLAEGVEVPLVGDFHFNGHLLLRKYPKMA
EALDKFRINPEHFAEMIRIAMDLGKPVRIGANWGSLDPALLTELMDRNAS
RPEPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLSAKVSKARDLVW
VYRELARRTQAPLHLGLTEAGMGVKGIVASAAALAPLLLEGIGDTIRVSL
TPSPKEPRTKEVEVAQEILQALGLRAFAPEVTSCPGCGRTTSTFFQELAE
EVSRRLKERLPEWRARYPGVEELKVAVMGCVVNGPGESKHAHIGISLPGA
GEEPKAPVYADGKLLTILKGEGIAEEFLRLVEDYVKTRFAPKA
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 chain2y0f Chain D Residue 501 [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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PDB2y0f Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Synthase (Gcpe) from Thermus Thermophilus.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		C297 P298 G299 C300 G342 C343 N346 G347 E350
Binding residue
(residue number reindexed from 1)		C284 P285 G286 C287 G329 C330 N333 G334 E337
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.7.3: (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin).
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0016491 oxidoreductase activity
GO:0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin)
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0141197 4-hydroxy-3-methylbut-2-enyl-diphosphate synthase activity (flavodoxin)
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
GO:0044237 cellular metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2y0f, PDBe:2y0f, PDBj:2y0f
PDBsum2y0f
PubMed21167158
UniProtQ72H18|ISPG_THET2 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (Gene Name=ispG)

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