SMTL ID : 3b04.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x 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(Non-covalent)

OOP.1: 27 residues within 4Å: Chain A: R.7, K.8, H.11, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, K.193, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297 Ligands: MG.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:M.67, A:W.225 Hydrogen bonds: A:R.7, A:H.11, A:T.65, A:G.66, A:M.67, A:S.96, A:S.96, A:N.125, A:N.125, A:N.157, A:Q.160, A:K.193, A:K.193, A:S.195, A:S.195, 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.155, A:R.277, A:R.277 Salt bridges: A:R.7, A:K.8, A:K.8, A:R.98, A:R.277 pi-Stacking: A:W.225 OOP.3: 28 residues within 4Å: Chain B: R.7, K.8, H.11, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, K.193, S.195, S.218, G.222, T.223, W.225, G.274, G.275, R.277, M.295, A.296, L.297 Ligands: MG.4 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:W.225, B:L.297 Hydrogen bonds: B:R.7, B:T.65, B:T.65, B:G.66, B:M.67, B:S.96, B:S.96, B:N.125, B:N.125, B:Q.130, B:N.157, B:Q.160, B:K.193, B:S.195, B:S.195, B:T.223, B:T.223, B:W.225, B:G.274, B:G.275, B:A.296, B:L.297 Water bridges: B:G.222, B:I.276, B:R.277 Salt bridges: B:R.7, B:K.8, B:K.8, B:R.98, B:R.277 pi-Stacking: B:W.225, B:W.225 OOP.5: 31 residues within 4Å: Chain C: R.7, K.8, H.11, V.12, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, 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: MG.6 34 PLIP interactions: 34 interactions with chain C Hydrophobic interactions: C:M.67, C:L.297, C:L.300 Hydrogen bonds: C:T.65, C:G.66, C:M.67, C:S.96, C:S.96, C:N.125, C:N.125, C:H.155, C:H.155, C:N.157, C:Q.160, 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:I.276, C:R.277 Salt bridges: C:R.7, C:R.7, C:K.8, C:K.8, C:H.11, C:R.98, C:R.277 pi-Stacking: C:W.225 OOP.7: 30 residues within 4Å: Chain D: R.7, K.8, H.11, V.12, A.15, T.65, G.66, M.67, G.95, S.96, R.98, N.125, Q.130, H.155, N.157, Q.160, 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 Ligands: MG.8 36 PLIP interactions: 36 interactions with chain D Hydrophobic interactions: D:V.12, D:A.15, D:M.67, D:L.297 Hydrogen bonds: D:T.65, D:G.66, D:M.67, D:S.96, D:S.96, D:N.125, D:N.125, D:Q.130, D:N.157, D:Q.160, D:K.193, D:K.193, D:S.195, D:S.195, 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:R.98, D:I.276, D:R.277 Salt bridges: D:R.7, D:R.7, D:K.8, D:K.8, D:R.98, D:R.277 pi-Stacking: D:W.225

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.161, Q.164 Ligands: OOP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: N.157, E.161, Q.164 Ligands: OOP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: N.157, E.161 Ligands: OOP.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: H.155, N.157, E.161 Ligands: OOP.7 No protein-ligand interaction detected (PLIP)

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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