Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 3b04 Chain D Binding Site BS02

Receptor Information
>3b04 Chain D (length=362) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRKVEHVEIAAFENVDGLSSSTFLNDVILVHQGFPGISFSEINTKTKFFR
KEISVPVMVTGMTGGRNELGRINKIIAEVAEKFGIPMGVGSQRVAIEKAE
ARESFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQDAIQMIEADAIAVH
LNPAQEVFQPEGEPEYQIYALEKLRDISKELSVPIIVKESGNGISMETAK
LLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAESAKNFLDWGVPTA
ASIMEVRYSVPDSFLVGSGGIRSGLDAAKAIALGADIAGMALPVLKSAIE
GKESLEQFFRKIIFELKAAMMLTGSKDVDALKKTSIVILGKLKEWAEYRG
INLSIYEKVRKR
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain3b04 Chain D Residue 1002 [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]
PDB3b04 Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H155 N157
Binding residue
(residue number reindexed from 1)		H150 N152
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3b04, PDBe:3b04, PDBj:3b04
PDBsum3b04
PubMed22158896
UniProtP61615|IDI2_SACSH Isopentenyl-diphosphate delta-isomerase (Gene Name=fni)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417