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Structure paper

TitleCovalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Journal, issue, pagesProc. Natl. Acad. Sci. USA, Vol. 108, Page 20461-20466, Year 2011
Publish dateJun 3, 2011 (structure data deposition date)
AuthorsNagai, T. / Unno, H. / Janczak, M.W. / Yoshimura, T. / Poulter, C.D. / Hemmi, H.
External linksProc. Natl. Acad. Sci. USA / PubMed:22158896
MethodsX-ray diffraction
Resolution2.2 - 2.3 Å
Structure data

PDB-3b03:
Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with vIPP.
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-3b04:
Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oIPP.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3b05:
Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP at 2.2A resolution.
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-3b06:
Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and DMAPP.
Method: X-RAY DIFFRACTION / Resolution: 2.29 Å

Chemicals

ChemComp-VNR:
1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-OOP:
1-deoxy-1-[(4aR)-4a-[(2R)-1-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylidenepentan-2-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol

ChemComp-FNR:
1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL

ChemComp-IPE:
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Isopentenyl pyrophosphate

ChemComp-DMA:
DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate

Source
  • sulfolobus shibatae (archaea)
KeywordsISOMERASE / TYPE 2 / IDI / FMN / ISOPENTENYL DIPHOSPHATE ISOMERASE / vIPP / oIPP / IPP / DMAPP

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