SMTL ID : 1p1j.1

Crystal structure of the 1L-myo-inositol 1-phosphate synthase complexed with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: S.323, G.324, Q.325, T.326, K.373, K.412, K.489 Ligands: NAI.2, GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.323, A:G.324, A:Q.325, A:T.326, A:T.326, A:K.327 Water bridges: A:K.412, A:K.412 Salt bridges: A:K.373, A:K.412, A:K.489 PO4.4: 9 residues within 4Å: Chain B: S.323, G.324, Q.325, T.326, K.373, K.412, K.489 Ligands: NAI.5, GOL.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.323, B:S.323, B:S.323, B:G.324, B:Q.325, B:T.326, B:T.326, B:K.327 Water bridges: B:K.412, B:K.412 Salt bridges: B:K.373, B:K.412, B:K.489 PO4.7: 9 residues within 4Å: Chain C: S.323, G.324, Q.325, T.326, K.373, K.412, K.489 Ligands: NAI.8, GOL.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.323, C:G.324, C:Q.325, C:T.326, C:K.327 Water bridges: C:K.412, C:K.412 Salt bridges: C:K.373, C:K.412, C:K.489 PO4.10: 9 residues within 4Å: Chain D: S.323, G.324, Q.325, T.326, K.373, K.412, K.489 Ligands: NAI.11, GOL.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.323, D:S.323, D:S.323, D:G.324, D:Q.325, D:T.326, D:K.327 Water bridges: D:K.412, D:K.412 Salt bridges: D:K.373, D:K.412, D:K.489

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

NAI.2: 31 residues within 4Å: Chain A: I.71, G.72, G.74, G.75, N.76, N.77, W.147, 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: PO4.1, GOL.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:L.321 Hydrogen bonds: A:G.74, A:N.76, 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:K.369, A:D.438 Water bridges: A:G.75, A:G.78, A:R.198, A:T.247, A:T.247, A:N.354, A:N.354, A:N.355, A:N.355, A:D.356 NAI.5: 30 residues within 4Å: Chain B: I.71, G.72, G.74, G.75, N.76, N.77, W.147, D.148, I.149, S.184, I.185, R.198, 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: PO4.4, GOL.6 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:L.321 Hydrogen bonds: 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:R.198, B:A.245, B:N.246, B:S.323, B:D.356, B:D.438 Water bridges: B:G.75, B:N.76, B:N.76, B:N.76, B:G.78, B:Y.187, B:T.244, B:T.247, B:T.247, B:N.354, B:N.355, B:N.355, B:D.356, B:D.356 NAI.8: 31 residues within 4Å: Chain C: I.71, G.72, G.74, G.75, N.76, N.77, W.147, 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: PO4.7, GOL.9 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:L.321 Hydrogen bonds: C:G.74, C:N.76, 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:A.245, C:N.246, C:N.246, C:S.323, C:N.355, C:D.356, C:K.369, C:D.438 Water bridges: C:G.75, C:G.78, C:R.198, C:T.244, C:T.247, C:N.354, C:N.354, C:N.355, C:N.355, C:D.356, C:D.438 NAI.11: 30 residues within 4Å: Chain D: I.71, G.72, G.74, G.75, N.76, N.77, W.147, D.148, I.149, S.184, I.185, R.198, 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: PO4.10, GOL.12 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:L.321 Hydrogen bonds: 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:R.198, D:A.245, D:N.246, D:T.247, D:S.323, D:D.356, D:D.438 Water bridges: D:G.75, D:N.76, D:N.76, D:N.76, D:G.78, D:Y.187, D:T.247, D:N.354, D:N.355, D:N.355, D:D.356, D:D.438

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: N.350, L.352, D.356, L.360, K.369, K.373, I.402, K.412, D.438 Ligands: PO4.1, NAI.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.350, A:D.356, A:K.373, A:K.412, A:K.412 Water bridges: A:D.356 GOL.6: 10 residues within 4Å: Chain B: N.350, L.352, D.356, K.369, K.373, I.402, K.412, D.438 Ligands: PO4.4, NAI.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.373, B:K.373, B:K.412, B:D.438 GOL.9: 11 residues within 4Å: Chain C: N.350, L.352, D.356, L.360, K.369, K.373, I.402, K.412, D.438 Ligands: PO4.7, NAI.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.350, C:D.356, C:K.373, C:K.412, C:K.412 Water bridges: C:D.438 GOL.12: 10 residues within 4Å: Chain D: N.350, L.352, D.356, K.369, K.373, I.402, K.412, D.438 Ligands: PO4.10, NAI.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.373, D:K.373, D:K.412, D:D.438

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, X. et al., Structures of NAD(+)- and NADH-bound 1-l-myo-inositol 1-phosphate synthase. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-07-08

Peptides

Inositol-3-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Inositol-3-phosphate synthase

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