Structure of PDB 4s3d Chain A Binding Site BS02

Receptor Information
>4s3d Chain A (length=402) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGS
EIVRLTVNDEEAAKAVPEIKRRLLAEGAEVPLVGDFHFNGHLLLRKYPKM
AEALDKFRINPGTLGRGRHKDEHFAEMIRIAMDLGKPVRIGANWGSLDPA
LLTELMDRNARRPEPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLS
AKVSKARDLVWVYRELARRTQAPLHLGLTEAGMGVKGIVASAAALAPLLL
EGIGDTIRVSLTPAPGEPRTKEVEVAQEILQALGLRAFAPEVTSCPGCGR
TTSTFFQELAEEVSRRLKERLPEWRARYPGVEELKVAVMGCVVNGPGESK
HAHIGISLPGAGEEPKAPVYADGKLLTILKGEGIAEEFLRLVEDYVKTRF
AP
Ligand information
Ligand IDDPO
InChIInChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
InChIKeyXPPKVPWEQAFLFU-UHFFFAOYSA-J
SMILES
SoftwareSMILES
CACTVS 3.370[O-][P]([O-])(=O)O[P]([O-])([O-])=O
OpenEye OEToolkits 1.7.2[O-]P(=O)([O-])OP(=O)([O-])[O-]
ACDLabs 12.01[O-]P([O-])(=O)OP([O-])([O-])=O
FormulaO7 P2
NameDIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain4s3d 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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PDB4s3d Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R56 R110 R141 N145 K204 T231 R260 S262
Binding residue
(residue number reindexed from 1)		R54 R108 R139 N143 K202 T229 R258 S260
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4s3d, PDBe:4s3d, PDBj:4s3d
PDBsum4s3d
PubMed25868383
UniProtQ5SLI8|ISPG_THET8 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (Gene Name=ispG)

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