SMTL ID : 2pny.1

Structure of Human Isopentenyl-diphosphate Delta-isomerase 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: S.105, E.134 Ligands: POP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.105, A:E.134, H2O.2, H2O.7

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

MN.2: 5 residues within 4Å: Chain A: H.59, H.70, H.107, E.165, E.167 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.59, A:H.70, A:H.107, A:E.165, A:E.167

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

POP.3: 11 residues within 4Å: Chain A: R.35, K.55, R.89, K.93, T.95, S.105, S.106, H.107, R.130, E.134 Ligands: CA.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:T.95, A:S.105, A:S.105, A:E.134 Water bridges: A:K.55, A:K.55, A:K.55, A:R.89, A:R.89, A:R.89, A:R.89, A:K.93, A:S.105, A:S.105, A:S.106 Salt bridges: A:R.35, A:K.55, A:K.55, A:R.89, A:K.93, A:K.93, A:H.107, A:H.107, A:R.130

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.222, K.242, H.244, R.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.222, A:K.242, A:H.244, A:R.245, A:R.245 GOL.5: 4 residues within 4Å: Chain A: Q.88, F.100, K.188, V.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.88, A:Q.88 GOL.6: 5 residues within 4Å: Chain A: H.154, H.155, K.156, R.245, V.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.246 Water bridges: A:K.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, J.R. et al., Structure of the human Isopentenyl-diphosphate Delta-isomerase 2. To be Published

Release Date

2007-05-29

Peptides

Isopentenyl-diphosphate Delta-isomerase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isopentenyl-diphosphate Delta-isomerase 2