SMTL ID : 3b06.1

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and DMAPP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

4 x 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(Non-covalent)

FNR.1: 21 residues within 4Å: Chain A: A.15, T.65, G.66, M.67, G.95, S.96, N.125, H.155, K.193, E.194, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297 Ligands: DMA.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.65, A:G.66, A:M.67, A:S.96, A:N.125, A:N.125, A:K.193, A:K.193, A:K.193, A:T.223, A:T.223, A:W.225, A:G.274, A:G.275, A:A.296, A:L.297 Water bridges: A:S.273, A:R.277, A:R.277 Salt bridges: A:R.277 pi-Stacking: A:W.225 FNR.4: 22 residues within 4Å: Chain B: A.15, T.65, G.66, M.67, G.95, S.96, N.125, H.155, K.193, E.194, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297, L.300 Ligands: DMA.5 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:A.15, B:M.67, B:L.300 Hydrogen bonds: B:T.65, B:G.66, B:S.96, B:N.125, B:N.125, B:K.193, B:K.193, B:K.193, B:T.223, B:T.223, B:W.225, B:G.274, B:G.275, B:A.296, B:L.297 Water bridges: B:M.67, B:G.222, B:S.273, B:I.276, B:R.277 Salt bridges: B:R.277 pi-Stacking: B:W.225, B:W.225 FNR.7: 22 residues within 4Å: Chain C: A.15, T.65, G.66, M.67, G.95, S.96, N.125, H.155, K.193, E.194, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297, L.300 Ligands: DMA.8 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:M.67, C:L.300 Hydrogen bonds: C:T.65, C:G.66, C:M.67, C:S.96, C:N.125, C:N.125, C:K.193, C:K.193, C:K.193, C:T.223, C:T.223, C:W.225, C:G.274, C:G.275, C:A.296, C:L.297 Water bridges: C:G.222, C:S.273, C:R.277, C:R.277 Salt bridges: C:R.277 pi-Stacking: C:W.225, C:W.225 FNR.10: 23 residues within 4Å: Chain D: A.15, T.65, G.66, M.67, G.95, S.96, N.125, H.155, K.193, E.194, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297, L.300 Ligands: DMA.11 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:A.15, D:M.67, D:L.300 Hydrogen bonds: D:T.65, D:G.66, D:M.67, D:S.96, D:N.125, D:N.125, D:K.193, D:K.193, D:K.193, D:S.218, D:T.223, D:T.223, D:W.225, D:G.274, D:G.275, D:A.296, D:L.297 Water bridges: D:G.222, D:S.273, D:R.277, D:R.277 Salt bridges: D:R.277 pi-Stacking: D:W.225, D:W.225

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.2: 15 residues within 4Å: Chain A: I.4, R.7, K.8, H.11, S.96, R.98, H.155, N.157, Q.160, E.161, Q.164, S.195, W.225 Ligands: FNR.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.225 Hydrogen bonds: A:S.96, A:S.96, A:Q.160, A:Q.164 Salt bridges: A:R.7, A:R.7, A:K.8, A:K.8, A:H.11, A:R.98, A:H.155 DMA.5: 15 residues within 4Å: Chain B: I.4, R.7, K.8, H.11, S.96, R.98, H.155, N.157, Q.160, E.161, Q.164, S.195, W.225 Ligands: FNR.4, MG.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.225 Hydrogen bonds: B:S.96, B:S.96, B:Q.160, B:Q.164 Salt bridges: B:R.7, B:R.7, B:K.8, B:K.8, B:H.11, B:R.98, B:H.155 DMA.8: 15 residues within 4Å: Chain C: I.4, R.7, K.8, H.11, S.96, R.98, H.155, N.157, Q.160, E.161, Q.164, S.195, W.225 Ligands: FNR.7, MG.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.225 Hydrogen bonds: C:S.96, C:S.96, C:Q.160, C:Q.164 Water bridges: C:G.127 Salt bridges: C:R.7, C:R.7, C:K.8, C:K.8, C:H.11, C:R.98, C:H.155 DMA.11: 15 residues within 4Å: Chain D: I.4, R.7, K.8, H.11, S.96, R.98, H.155, N.157, Q.160, E.161, Q.164, S.195, W.225 Ligands: FNR.10, MG.12 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.225 Hydrogen bonds: D:S.96, D:S.96, D:Q.160, D:Q.164 Salt bridges: D:R.7, D:R.7, D:K.8, D:K.8, D:H.11, D:R.98, D:H.155

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: R.98, N.157, E.161 Ligands: DMA.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.161 MG.6: 4 residues within 4Å: Chain B: R.98, N.157, E.161 Ligands: DMA.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.161 MG.9: 4 residues within 4Å: Chain C: Q.130, N.157, E.161 Ligands: DMA.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.161 MG.12: 4 residues within 4Å: Chain D: R.98, N.157, E.161 Ligands: DMA.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagai, T. et al., Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-11-02

Peptides

Isopentenyl-diphosphate delta-isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isopentenyl-diphosphate delta-isomerase

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