Structure of PDB 4s23 Chain B Binding Site BS02

Receptor Information
>4s23 Chain B (length=405) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAG
SEIVRLTVNDEEAAKAVPEIKRRLLAEGVEVPLVGDFHFNGHLLLRKYPK
MAEALDKFRINPGTLGRGRHKDEHFAEMIRIAMDLGKPVRIGANWGSLDP
ALLTELMDRNASRPEPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVL
SAKVSKARDLVWVYRELARRTQAPLHLGLTEAGMGVKGIVASAAALAPLL
LEGIGDTIRVSLTPSPKEPRTKEVEVAQEILQALGLRAFAPEVTSCPGCG
RTTSTFFQELAEEVSRRLKERLPEWRARYPGVEELKVAVMGCVVNGPGES
KHAHIGISLPGAGEEPKAPVYADGKLLTILKGEGIAEEFLRLVEDYVKTR
FAPKA
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 chain4s23 Chain B Residue 503 [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]
PDB4s23 Structure of the GcpE-HMBPP complex from Thermus thermophilius.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		R56 H89 R110 N145 K204 T231 R260 S262
Binding residue
(residue number reindexed from 1)		R55 H88 R109 N144 K203 T230 R259 S261
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4s23, PDBe:4s23, PDBj:4s23
PDBsum4s23
PubMed25660452
UniProtQ5SLI8|ISPG_THET8 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (Gene Name=ispG)

[Back to BioLiP]