SMTL ID : 2b2k.1

structure of Y104F IDI-1 mutant in complex with EIPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 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: EIP.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: 3 residues within 4Å: Chain B: C.67, E.87 Ligands: EIP.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 EIP: 4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE(Covalent)

EIP.3: 15 residues within 4Å: Chain A: K.21, A.34, F.35, R.51, K.55, C.67, G.68, H.69, R.83, E.87, F.104, E.114, E.116, C.118 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.34, A:F.104 Hydrogen bonds: A:E.4 Water bridges: A:K.21, A:R.51, A:R.51, A:R.51, A:K.55, A:K.55, A:H.69, 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 EIP.6: 15 residues within 4Å: Chain B: K.21, A.34, R.51, K.55, C.67, G.68, H.69, R.83, E.87, F.104, E.114, E.116, C.118, W.161 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.34, B:E.116 Hydrogen bonds: B:H.69 Water bridges: B:R.51, B:K.55, B:C.67, B:E.135 Salt bridges: B:K.21, B:R.51, B:K.55, B:K.55, B:H.69, B:H.69, B:R.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Ruyck, J. et al., Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography. J.Biol.Chem. (2006)

Release Date

2006-09-05

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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