SMTL ID : 2zrv.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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: 20 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 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.15 Hydrogen bonds: A:T.65, A:G.66, A:S.96, A:N.125, A:N.125, A:K.193, A:K.193, A:K.193, A:S.218, A:T.223, A:T.223, A:W.225, A:G.274, A:G.275, A:A.296, A:L.297 Water bridges: A:H.11, A:M.67, A:S.195, A:S.195, A:G.222, A:S.273, A:R.277, A:R.277 Salt bridges: A:R.277 pi-Stacking: A:W.225 FNR.2: 21 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 28 PLIP interactions: 28 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:S.218, B:T.223, B:T.223, B:W.225, B:G.274, B:G.275, B:A.296, B:L.297 Water bridges: B:K.8, B:M.67, B:S.195, B:S.195, B:G.222, B:I.276, B:R.277 Salt bridges: B:R.277 pi-Stacking: B:W.225 FNR.3: 20 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 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:A.15, C:M.67 Hydrogen bonds: C:T.65, C:G.66, C:S.96, C:N.125, C:N.125, C:K.193, C:K.193, C:K.193, C:S.218, C:T.223, C:T.223, C:W.225, C:G.274, C:G.275, C:A.296, C:L.297 Water bridges: C:K.8, C:M.67, C:Q.160, C:S.195, C:S.195, C:G.222, C:R.277, C:R.277 Salt bridges: C:R.277 pi-Stacking: C:W.225 FNR.4: 20 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.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:A.15, D:M.67 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:S.195, D:S.195, D:G.222, D:R.277, D:R.277 Salt bridges: D:R.277 pi-Stacking: D:W.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, H. et al., New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase. J.Biol.Chem. (2009)

Release Date

2009-01-20

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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