Structure of PDB 2zrx Chain D Binding Site BS02

Receptor Information
>2zrx Chain D (length=364) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIVNRKVEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTK
FFRKEISVPVMVTGMTGGRNELGRINKIIAEVAEKFGIPMGVGSQRVAIE
KAEARESFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAI
AVHLNPAQEVFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISME
TAKLLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGV
PTAASIMEVRYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKS
AIEGKESLEQFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAE
YRGINLSIYEKVRK
Ligand information
Ligand IDDMA
InChIInChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyCBIDRCWHNCKSTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCOP(=O)(O)OP(=O)(O)O)C
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/C)C)O)(O)O
OpenEye OEToolkits 1.5.0CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
CACTVS 3.341CC(C)=CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCO[P](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O7 P2
NameDIMETHYLALLYL DIPHOSPHATE
ChEMBLCHEMBL343480
DrugBankDB01785
ZINCZINC000008215740
PDB chain2zrx Chain D Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zrx New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R7 K8 S96 R98 H155 Q160 W225
Binding residue
(residue number reindexed from 1)		R5 K6 S94 R96 H153 Q158 W223
Annotation score5
Enzymatic activity
Enzyme Commision number 5.3.3.2: isopentenyl-diphosphate Delta-isomerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004452 isopentenyl-diphosphate delta-isomerase activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
GO:0070402 NADPH binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zrx, PDBe:2zrx, PDBj:2zrx
PDBsum2zrx
PubMed19158086
UniProtP61615|IDI2_SACSH Isopentenyl-diphosphate delta-isomerase (Gene Name=fni)

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