SMTL ID : 1vko.1

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: N.87, N.88, N.358, D.412, D.440, S.441 Ligands: NAD.6 No protein-ligand interaction detected (PLIP) K.8: 7 residues within 4Å: Chain B: N.87, N.88, N.358, D.412, D.440, S.441 Ligands: NAD.13 No protein-ligand interaction detected (PLIP) K.15: 7 residues within 4Å: Chain C: N.87, N.88, N.358, D.412, D.440, S.441 Ligands: NAD.20 No protein-ligand interaction detected (PLIP) K.22: 7 residues within 4Å: Chain D: N.87, N.88, N.358, D.412, D.440, S.441 Ligands: NAD.27 No protein-ligand interaction detected (PLIP)

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: H.127, F.502 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: Y.116 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: H.127, F.502 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: Y.116 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: H.127, F.502 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: Y.116 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain D: H.127, F.502 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: Y.116 Ligand excluded by PLIP

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 2 residues within 4Å: Chain A: S.132 Chain C: K.47 Ligand excluded by PLIP IOD.5: 5 residues within 4Å: Chain A: F.392, P.393, D.394, A.395, K.396 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain B: S.132 Chain D: K.47 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain B: F.392, P.393, D.394, A.395, K.396 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: K.47 Chain C: S.132 Ligand excluded by PLIP IOD.19: 5 residues within 4Å: Chain C: F.392, P.393, D.394, A.395, K.396 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain B: K.47 Chain D: S.132 Ligand excluded by PLIP IOD.26: 5 residues within 4Å: Chain D: F.392, P.393, D.394, A.395, K.396 Ligand excluded by PLIP

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 29 residues within 4Å: Chain A: V.82, G.83, G.85, G.86, N.87, N.88, W.159, D.160, I.161, S.196, I.197, R.210, T.248, A.249, N.250, T.251, G.299, S.300, D.324, F.325, S.327, N.359, D.360, K.373, D.440, A.444, K.484 Ligands: K.1, POP.7 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.325 Hydrogen bonds: A:G.83, A:G.85, A:N.87, A:N.88, A:N.88, A:I.161, A:S.196, A:I.197, A:R.210, A:R.210, A:T.248, A:A.249, A:N.250, A:N.250, A:T.251, A:T.251, A:S.327, A:N.359, A:D.360, A:K.373, A:D.440 Water bridges: A:G.86, A:G.89, A:Y.199, A:N.359, A:N.359, A:D.360, A:D.360, A:D.440 pi-Stacking: A:F.325 NAD.13: 29 residues within 4Å: Chain B: V.82, G.83, G.85, G.86, N.87, N.88, W.159, D.160, I.161, S.196, I.197, R.210, T.248, A.249, N.250, T.251, G.299, S.300, D.324, F.325, S.327, N.359, D.360, K.373, D.440, A.444, K.484 Ligands: K.8, POP.14 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:F.325 Hydrogen bonds: B:G.83, B:G.85, B:N.87, B:N.88, B:N.88, B:I.161, B:S.196, B:I.197, B:R.210, B:R.210, B:T.248, B:A.249, B:N.250, B:N.250, B:T.251, B:T.251, B:S.327, B:N.359, B:D.360, B:K.373, B:D.440 Water bridges: B:G.86, B:G.89, B:Y.199, B:N.359, B:N.359, B:D.360, B:D.360, B:D.440 pi-Stacking: B:F.325 NAD.20: 29 residues within 4Å: Chain C: V.82, G.83, G.85, G.86, N.87, N.88, W.159, D.160, I.161, S.196, I.197, R.210, T.248, A.249, N.250, T.251, G.299, S.300, D.324, F.325, S.327, N.359, D.360, K.373, D.440, A.444, K.484 Ligands: K.15, POP.21 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:F.325 Hydrogen bonds: C:G.83, C:G.85, C:N.87, C:N.88, C:N.88, C:I.161, C:S.196, C:I.197, C:R.210, C:R.210, C:A.249, C:N.250, C:N.250, C:T.251, C:S.327, C:N.359, C:D.360, C:K.373, C:D.440 Water bridges: C:G.86, C:G.89, C:Y.199, C:N.358, C:N.359, C:N.359, C:D.360, C:D.360 pi-Stacking: C:F.325 NAD.27: 29 residues within 4Å: Chain D: V.82, G.83, G.85, G.86, N.87, N.88, W.159, D.160, I.161, S.196, I.197, R.210, T.248, A.249, N.250, T.251, G.299, S.300, D.324, F.325, S.327, N.359, D.360, K.373, D.440, A.444, K.484 Ligands: K.22, POP.28 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:F.325 Hydrogen bonds: D:G.83, D:G.85, D:N.87, D:N.88, D:N.88, D:I.161, D:S.196, D:I.197, D:R.210, D:R.210, D:A.249, D:N.250, D:N.250, D:T.251, D:S.327, D:N.359, D:D.360, D:K.373, D:D.440 Water bridges: D:G.86, D:G.89, D:Y.199, D:N.358, D:N.359, D:N.359, D:D.360, D:D.360 pi-Stacking: D:F.325

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

POP.7: 11 residues within 4Å: Chain A: K.326, S.327, G.328, Q.329, T.330, K.331, K.373, K.377, K.414, K.484 Ligands: NAD.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.327, A:S.327, A:G.328, A:Q.329, A:T.330, A:K.331 Water bridges: A:D.440 Salt bridges: A:K.373, A:K.377, A:K.377, A:K.414, A:K.414, A:K.484, A:K.484 POP.14: 11 residues within 4Å: Chain B: K.326, S.327, G.328, Q.329, T.330, K.331, K.373, K.377, K.414, K.484 Ligands: NAD.13 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.327, B:S.327, B:G.328, B:Q.329, B:T.330, B:K.331 Water bridges: B:D.440 Salt bridges: B:K.373, B:K.377, B:K.377, B:K.414, B:K.414, B:K.484, B:K.484 POP.21: 11 residues within 4Å: Chain C: K.326, S.327, G.328, Q.329, T.330, K.331, K.373, K.377, K.414, K.484 Ligands: NAD.20 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.327, C:S.327, C:G.328, C:Q.329, C:T.330, C:T.330, C:K.331 Salt bridges: C:K.373, C:K.377, C:K.377, C:K.414, C:K.414, C:K.484, C:K.484 POP.28: 11 residues within 4Å: Chain D: K.326, S.327, G.328, Q.329, T.330, K.331, K.373, K.377, K.414, K.484 Ligands: NAD.27 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.327, D:S.327, D:G.328, D:Q.329, D:T.330, D:T.330, D:K.331 Salt bridges: D:K.373, D:K.377, D:K.377, D:K.414, D:K.414, D:K.484, D:K.484

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution. To be published

Release Date

2004-08-17

Peptides

inositol-3-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

inositol-3-phosphate synthase