SMTL ID : 1rm0.1

Crystal Structure of Myo-Inositol 1-Phosphate Synthase From Saccharomyces cerevisiae In Complex With NAD+ and 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: N.76, N.77, N.354, D.410, S.439 Ligands: NAI.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.439 MN.5: 6 residues within 4Å: Chain C: N.76, N.77, N.354, D.410, S.439 Ligands: NAI.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.439

2 x D6P: (3,4,5,7-TETRAHYDROXY-HEPT-1-ENYL)-PHOSPHONIC ACID(Non-covalent)

D6P.2: 17 residues within 4Å: Chain A: K.322, S.323, G.324, Q.325, T.326, K.327, N.350, L.352, D.356, L.360, K.369, K.373, I.402, K.412, D.438, K.489 Ligands: NAI.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.352, A:L.360 Hydrogen bonds: A:S.323, A:S.323, A:G.324, A:Q.325, A:T.326, A:T.326, A:K.327, A:D.356, A:K.369, A:K.369, A:K.373, A:K.412, A:D.438, A:K.489 Water bridges: A:D.356, A:D.356 D6P.6: 17 residues within 4Å: Chain C: K.322, S.323, G.324, Q.325, T.326, K.327, N.350, L.352, D.356, L.360, K.369, K.373, I.402, K.412, D.438, K.489 Ligands: NAI.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.352, C:L.360 Hydrogen bonds: C:S.323, C:S.323, C:G.324, C:Q.325, C:T.326, C:K.327, C:D.356, C:K.369, C:K.369, C:K.373, C:K.412, C:D.438, C:K.489 Water bridges: C:D.438, C:D.438

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 30 residues within 4Å: Chain A: I.71, G.72, G.74, G.75, N.76, N.77, D.148, I.149, S.184, I.185, R.198, W.243, T.244, A.245, N.246, T.247, P.277, G.295, S.296, D.320, L.321, S.323, N.355, D.356, K.369, D.438, A.442, K.489 Ligands: MN.1, D6P.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.321, A:A.442 Hydrogen bonds: A:G.74, A:N.76, A:N.77, A:N.77, A:I.149, A:S.184, A:I.185, A:R.198, A:R.198, A:A.245, A:N.246, A:N.246, A:T.247, A:S.323, A:N.355, A:D.356, A:D.356, A:D.356 Water bridges: A:G.75, A:G.78, A:Y.187, A:T.247, A:T.247, A:N.354, A:N.355, A:N.355, A:D.356 NAI.4: 30 residues within 4Å: Chain B: I.71, G.72, G.74, G.75, N.76, N.77, D.148, I.149, S.184, I.185, I.191, R.198, W.243, T.244, A.245, N.246, T.247, P.277, G.295, S.296, P.297, D.320, L.321, S.323, N.355, D.356, K.369, D.438, A.442, K.489 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.321 Hydrogen bonds: B:G.72, B:G.74, B:G.74, B:N.76, B:N.77, B:N.77, B:I.149, B:S.184, B:I.185, B:R.198, B:T.244, B:N.246, B:N.246, B:T.247, B:T.247, B:D.356 Water bridges: B:G.75, B:N.76, B:N.76, B:Y.187, B:R.198, B:N.354, B:N.355, B:N.355 NAI.7: 30 residues within 4Å: Chain C: I.71, G.72, G.74, G.75, N.76, N.77, D.148, I.149, S.184, I.185, R.198, W.243, T.244, A.245, N.246, T.247, P.277, G.295, S.296, D.320, L.321, S.323, N.355, D.356, K.369, D.438, A.442, K.489 Ligands: MN.5, D6P.6 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:L.321, C:A.442 Hydrogen bonds: C:G.74, C:N.76, C:N.77, C:N.77, C:I.149, C:S.184, C:I.185, C:R.198, C:R.198, C:T.244, C:A.245, C:N.246, C:N.246, C:S.323, C:N.355, C:D.356, C:D.356 Water bridges: C:G.75, C:G.78, C:Y.187, C:T.247, C:N.355, C:N.355, C:D.356, C:D.356, C:D.438, C:D.438 NAI.8: 30 residues within 4Å: Chain D: I.71, G.72, G.74, G.75, N.76, N.77, D.148, I.149, S.184, I.185, I.191, R.198, W.243, T.244, A.245, N.246, T.247, P.277, G.295, S.296, P.297, D.320, L.321, S.323, N.355, D.356, K.369, D.438, A.442, K.489 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:L.321 Hydrogen bonds: D:G.72, D:G.74, D:G.74, D:N.76, D:N.77, D:N.77, D:I.149, D:S.184, D:I.185, D:R.198, D:N.246, D:N.246, D:T.247, D:T.247, D:T.247, D:D.356 Water bridges: D:G.75, D:N.76, D:N.76, D:Y.187, D:R.198, D:N.354, D:N.355, D:N.355, D:D.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, X. et al., The structure of the 1L-myo-inositol-1-phosphate synthase-NAD+-2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate complex demands a revision of the enzyme mechanism. J.Biol.Chem. (2004)

Release Date

2004-05-25

Peptides

myo-inositol-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

myo-inositol-phosphate synthase

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