SMTL ID : 3dh7.1

Structure of T. thermophilus IDI-2 in complex with PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: C.14, A.65, M.66, T.67, S.95, N.123, H.152, K.187, E.188, V.189, G.190, G.216, T.217, W.219, G.263, G.264, Y.266, V.284, A.285, R.286, P.287, L.289 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:M.66, A:R.286 Hydrogen bonds: A:A.65, A:A.65, A:T.67, A:T.67, A:S.95, A:H.152, A:K.187, A:K.187, A:T.217, A:S.262, A:G.263, A:G.264, A:Y.266, A:A.285, A:R.286 pi-Stacking: A:H.152, A:W.219, A:W.219 FMN.2: 21 residues within 4Å: Chain B: L.11, C.14, A.65, M.66, T.67, S.95, N.123, H.152, K.187, V.189, G.190, G.216, T.217, W.219, G.263, G.264, Y.266, A.285, R.286, P.287, L.289 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.11, B:M.66, B:W.219, B:R.286 Hydrogen bonds: B:A.65, B:A.65, B:S.95, B:N.123, B:K.187, B:E.188, B:T.217, B:T.217, B:G.264, B:Y.266, B:A.285, B:R.286 Water bridges: B:G.263 pi-Stacking: B:W.219 FMN.4: 20 residues within 4Å: Chain C: C.14, A.65, M.66, T.67, S.95, H.152, K.187, V.189, G.190, G.216, T.217, W.219, G.263, G.264, Y.266, V.284, A.285, R.286, P.287, L.289 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:M.66, C:R.286, C:L.289 Hydrogen bonds: C:A.65, C:T.67, C:S.95, C:K.187, C:K.187, C:T.217, C:S.262, C:G.263, C:G.264, C:Y.266, C:Y.266, C:A.285, C:R.286, C:R.286 pi-Stacking: C:W.219, C:W.219 FMN.5: 22 residues within 4Å: Chain D: C.14, A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, A.212, G.216, T.217, W.219, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:M.66, D:W.219, D:R.286 Hydrogen bonds: D:A.65, D:A.65, D:S.95, D:N.123, D:N.123, D:H.152, D:K.187, D:K.187, D:T.217, D:T.217, D:W.219, D:S.262, D:G.263, D:G.264, D:A.285, D:R.286, D:R.286 pi-Stacking: D:W.219

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 6 residues within 4Å: Chain B: S.95, R.97, L.124, G.125, Q.128, H.152 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.95 Water bridges: B:Q.157 Salt bridges: B:R.97, B:R.97, B:H.152, B:H.152 POP.6: 7 residues within 4Å: Chain D: S.95, R.97, L.124, G.125, L.126, Q.128, H.152 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.95, D:S.95, D:G.125, D:Q.128 Water bridges: D:Q.161, D:Q.161 Salt bridges: D:R.97, D:H.152, D:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Ruyck, J. et al., Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate. Biochemistry (2008)

Release Date

2008-09-23

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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