SMTL ID : 1nfs.1

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.25, H.32, H.69, E.114, E.116 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.25, A:H.32, A:H.69, A:E.114, A:E.116 MN.4: 5 residues within 4Å: Chain B: H.25, H.32, H.69, E.114, E.116 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.25, B:H.32, B:H.69, B:E.114, B:E.116

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: C.67, E.87 Ligands: DED.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.67, A:E.87, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: C.67, R.83, E.87 Ligands: DED.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.67, B:E.87, H2O.3, H2O.3

2 x DED: 2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE(Non-covalent)

DED.3: 15 residues within 4Å: Chain A: K.21, F.35, R.51, K.55, C.67, G.68, H.69, R.83, E.87, Y.104, E.114, E.116, C.118, W.161 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:H.69 Water bridges: A:R.51, A:R.51, A:R.51, A:R.51, A:C.67, A:E.135 Salt bridges: A:K.21, A:R.51, A:K.55, A:K.55, A:H.69, A:H.69, A:R.83, A:E.114, A:E.116 DED.6: 16 residues within 4Å: Chain B: K.21, A.34, F.35, R.51, K.55, C.67, G.68, H.69, R.83, E.87, Y.104, E.114, E.116, C.118, W.161 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.69, B:Y.104 Water bridges: B:K.55, B:K.55, B:C.67 Salt bridges: B:K.21, B:R.51, B:K.55, B:K.55, B:H.69, B:H.69, B:R.83, B:E.114, B:E.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wouters, J. et al., Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors. J.Biol.Chem. (2003)

Release Date

2003-06-24

Peptides

ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE

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