SMTL ID : 2i6k.1 (1 other biounit)

Crystal structure of human type I IPP isomerase complexed with a substrate analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.48, H.59, H.96, E.154, E.156 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.48, A:H.59, A:H.96, A:E.154, A:E.156

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: C.94, E.123 Ligands: EA2.4 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:C.94, A:E.123, H2O.1, H2O.2, EA2.4 MG.3: 2 residues within 4Å: Chain A: E.105, S.107 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.105, A:S.107, H2O.1, H2O.3, H2O.3

1 x EA2: AMINOETHANOLPYROPHOSPHATE(Non-covalent)

EA2.4: 14 residues within 4Å: Chain A: K.44, R.78, K.82, T.84, C.94, S.95, H.96, R.119, E.123, Y.144, E.154, E.156, W.204 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.84, A:S.95, A:Y.144, A:Y.144 Water bridges: A:K.44, A:R.78, A:C.94, A:R.119, A:R.119 Salt bridges: A:K.44, A:K.44, A:R.78, A:K.82, A:K.82, A:H.96, A:H.96, A:R.119

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 4 residues within 4Å: Chain A: D.36, E.106, R.141, Y.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.36, A:D.36, A:Y.159 Salt bridges: A:R.141 ACY.6: 3 residues within 4Å: Chain A: D.33, E.34, N.35 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.34 Hydrogen bonds: A:E.34 ACY.7: 5 residues within 4Å: Chain A: L.191, A.194, A.195, I.201, K.206 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Crystal structures of human IPP isomerase: new insights into the catalytic mechanism. J.Mol.Biol. (2007)

Release Date

2007-06-05

Peptides

Isopentenyl-diphosphate delta-isomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isopentenyl-diphosphate delta-isomerase 1

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