Structure of PDB 4s39 Chain A Binding Site BS02

Receptor Information
>4s39 Chain A (length=401) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGSE
IVRLTVNDEEAAKAVPEIKRRLLAEGAEVPLVGDFHFNGHLLLRKYPKMA
EALDKFRINPGTLGRGRHKDEHFAEMIRIAMDLGKPVRIGANWGSLDPAL
LTELMDRNARRPEPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLSA
KVSKARDLVWVYRELARRTQAPLHLGLTEAGMGVKGIVASAAALAPLLLE
GIGDTIRVSLTPAPGEPRTKEVEVAQEILQALGLRAFAPEVTSCPGCGRT
TSTFFQELAEEVSRRLKERLPEWRARYPGVEELKVAVMGCVVNGPGESKH
AHIGISLPGAGEEPKAPVYADGKLLTILKGEGIAEEFLRLVEDYVKTRFA
P
Ligand information
Ligand IDH6P
InChIInChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)/b5-2+
InChIKeyMDSIZRKJVDMQOQ-GORDUTHDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(=CCOP(=O)(O)OP(=O)(O)O)CO
ACDLabs 12.01O=P(O)(O)OP(=O)(OC\C=C(/C)CO)O
CACTVS 3.370CC(CO)=CCO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.2C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)/CO
CACTVS 3.370C\C(CO)=C/CO[P](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O8 P2
Name(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
ChEMBLCHEMBL145233
DrugBank
ZINCZINC000008436838
PDB chain4s39 Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4s39 Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).
Resolution1.3 Å
Binding residue
(original residue number in PDB)		R56 H89 R110 R141 N145 K204 T231 R260 S262
Binding residue
(residue number reindexed from 1)		R53 H86 R107 R138 N142 K201 T228 R257 S259
Annotation score5
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4s39, PDBe:4s39, PDBj:4s39
PDBsum4s39
PubMed25868383
UniProtQ5SLI8|ISPG_THET8 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (Gene Name=ispG)

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