SMTL ID : 3qvt.1

L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus wild-type with the intermediate 5-keto 1-phospho glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: K.360, T.372, N.373, V.374 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.372, A:T.372, A:N.373, A:V.374 Water bridges: A:T.372 Salt bridges: A:K.360 PO4.4: 10 residues within 4Å: Chain A: K.227, T.228, G.229, E.230, T.231, K.278, K.306, K.367 Ligands: NAI.2, KPG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.228, A:G.229, A:E.230, A:T.231, A:T.231, A:T.231 Water bridges: A:T.228, A:T.228 Salt bridges: A:K.278, A:K.306, A:K.367 PO4.8: 4 residues within 4Å: Chain B: K.360, T.372, N.373, V.374 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.372, B:T.372, B:N.373, B:V.374 Water bridges: B:T.372 Salt bridges: B:K.360 PO4.11: 10 residues within 4Å: Chain B: K.227, T.228, G.229, E.230, T.231, K.278, K.306, K.367 Ligands: NAI.9, KPG.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.228, B:G.229, B:E.230, B:T.231, B:T.231, B:T.231 Water bridges: B:T.228, B:T.228 Salt bridges: B:K.278, B:K.306, B:K.367 PO4.15: 4 residues within 4Å: Chain C: K.360, T.372, N.373, V.374 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.372, C:T.372, C:T.372, C:N.373, C:V.374 Salt bridges: C:K.360 PO4.18: 10 residues within 4Å: Chain C: K.227, T.228, G.229, E.230, T.231, K.278, K.306, K.367 Ligands: NAI.16, KPG.19 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.228, C:G.229, C:E.230, C:T.231, C:T.231 Salt bridges: C:K.278, C:K.306, C:K.367 PO4.22: 4 residues within 4Å: Chain D: K.360, T.372, N.373, V.374 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.372, D:T.372, D:T.372, D:N.373, D:V.374 Salt bridges: D:K.360 PO4.25: 10 residues within 4Å: Chain D: K.227, T.228, G.229, E.230, T.231, K.278, K.306, K.367 Ligands: NAI.23, KPG.26 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.228, D:G.229, D:E.230, D:T.231, D:T.231 Salt bridges: D:K.278, D:K.306, D:K.367

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

NAI.2: 34 residues within 4Å: Chain A: V.6, G.7, Y.9, G.10, I.11, V.12, H.56, E.57, I.58, R.59, T.99, A.100, C.103, I.107, L.110, V.147, A.148, S.149, T.150, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336, K.367 Ligands: PO4.4, KPG.5 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.228 Hydrogen bonds: A:G.7, A:Y.9, A:I.11, A:V.12, A:I.58, A:R.59, A:R.59, A:R.59, A:T.99, A:A.148, A:S.149, A:T.150, A:Y.185, A:T.228, A:D.261, A:D.304, A:D.332 Water bridges: A:G.10, A:S.13, A:H.71, A:T.228, A:D.261, A:D.261, A:D.261 NAI.9: 34 residues within 4Å: Chain B: V.6, G.7, Y.9, G.10, I.11, V.12, H.56, E.57, I.58, R.59, T.99, A.100, C.103, I.107, L.110, V.147, A.148, S.149, T.150, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336, K.367 Ligands: PO4.11, KPG.12 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.228 Hydrogen bonds: B:G.7, B:Y.9, B:I.11, B:V.12, B:I.58, B:R.59, B:R.59, B:R.59, B:T.99, B:A.148, B:S.149, B:T.150, B:Y.185, B:T.228, B:D.261, B:D.304, B:D.332 Water bridges: B:G.10, B:S.13, B:H.71, B:T.228, B:D.261, B:D.261, B:D.261 NAI.16: 34 residues within 4Å: Chain C: V.6, G.7, Y.9, G.10, I.11, V.12, H.56, E.57, I.58, R.59, T.99, A.100, C.103, I.107, L.110, V.147, A.148, S.149, T.150, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336, K.367 Ligands: PO4.18, KPG.19 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:T.228 Hydrogen bonds: C:G.7, C:Y.9, C:I.11, C:V.12, C:I.58, C:R.59, C:R.59, C:R.59, C:T.99, C:A.148, C:S.149, C:T.150, C:T.150, C:T.228, C:T.228, C:D.261, C:D.304 Water bridges: C:G.10, C:S.13, C:E.151, C:D.261, C:D.261, C:D.261 NAI.23: 34 residues within 4Å: Chain D: V.6, G.7, Y.9, G.10, I.11, V.12, H.56, E.57, I.58, R.59, T.99, A.100, C.103, I.107, L.110, V.147, A.148, S.149, T.150, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336, K.367 Ligands: PO4.25, KPG.26 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:T.228 Hydrogen bonds: D:G.7, D:Y.9, D:I.11, D:V.12, D:I.58, D:R.59, D:R.59, D:R.59, D:T.99, D:A.148, D:S.149, D:T.150, D:T.150, D:T.228, D:T.228, D:D.261, D:D.304 Water bridges: D:G.10, D:S.13, D:E.151, D:D.261, D:D.261, D:D.261

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 3 residues within 4Å: Chain A: E.131, E.132, K.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.131, A:K.135 PG4.10: 3 residues within 4Å: Chain B: E.131, E.132, K.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.131, B:K.135 PG4.17: 3 residues within 4Å: Chain C: E.131, E.132, K.135 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.135 PG4.24: 3 residues within 4Å: Chain D: E.131, E.132, K.135 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.135

4 x KPG: [(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate(Non-covalent)

KPG.5: 18 residues within 4Å: Chain A: D.225, T.228, G.229, E.230, T.231, L.232, N.255, L.257, D.261, L.265, K.274, K.278, I.296, K.306, D.332, K.367 Ligands: NAI.2, PO4.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.228, A:T.228, A:G.229, A:E.230, A:E.230, A:T.231, A:T.231, A:T.231, A:L.232, A:N.255, A:K.274, A:K.306, A:D.332, A:K.367 Salt bridges: A:K.278, A:K.278, A:K.306, A:K.306, A:K.367 KPG.12: 18 residues within 4Å: Chain B: D.225, T.228, G.229, E.230, T.231, L.232, N.255, L.257, D.261, L.265, K.274, K.278, I.296, K.306, D.332, K.367 Ligands: NAI.9, PO4.11 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.228, B:T.228, B:G.229, B:E.230, B:E.230, B:T.231, B:T.231, B:T.231, B:L.232, B:N.255, B:K.274, B:K.306, B:D.332, B:K.367 Salt bridges: B:K.278, B:K.278, B:K.306, B:K.306, B:K.367 KPG.19: 18 residues within 4Å: Chain C: D.225, T.228, G.229, E.230, T.231, L.232, N.255, L.257, D.261, L.265, K.274, K.278, I.296, K.306, D.332, K.367 Ligands: NAI.16, PO4.18 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.228, C:G.229, C:E.230, C:T.231, C:T.231, C:L.232, C:N.255, C:K.274, C:K.306, C:D.332, C:K.367 Salt bridges: C:K.278, C:K.278, C:K.306, C:K.306, C:K.367 KPG.26: 18 residues within 4Å: Chain D: D.225, T.228, G.229, E.230, T.231, L.232, N.255, L.257, D.261, L.265, K.274, K.278, I.296, K.306, D.332, K.367 Ligands: NAI.23, PO4.25 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.228, D:G.229, D:E.230, D:T.231, D:T.231, D:L.232, D:N.255, D:K.274, D:K.306, D:D.332, D:K.367 Salt bridges: D:K.278, D:K.278, D:K.306, D:K.306, D:K.367

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: N.305, D.329, I.331 Chain B: K.323 Chain D: K.320, L.321, M.322, K.323 Ligands: GOL.20 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:K.323, A:N.305, B:K.323, B:K.323 GOL.13: 9 residues within 4Å: Chain A: K.323 Chain B: N.305, D.329, I.331 Chain C: K.320, L.321, M.322, K.323 Ligands: GOL.27 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:K.323, B:N.305, A:K.323, A:K.323 GOL.20: 9 residues within 4Å: Chain B: K.320, L.321, M.322, K.323 Chain C: N.305, D.329, I.331 Chain D: K.323 Ligands: GOL.6 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:K.323, D:K.323, C:N.305, B:K.323 GOL.27: 9 residues within 4Å: Chain A: K.320, L.321, M.322, K.323 Chain C: K.323 Chain D: N.305, D.329, I.331 Ligands: GOL.13 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:K.323, C:K.323, D:N.305, A:K.323

4 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: D.329 Chain B: Y.325 Chain C: D.329 Chain D: Y.325 Ligands: NA.21 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:Y.325, B:Y.325, C:D.329 Water bridges: D:K.323, B:K.323 NA.14: 5 residues within 4Å: Chain A: Y.325 Chain B: D.329 Chain C: Y.325 Chain D: D.329 Ligands: NA.28 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B Water bridges: C:K.323, A:K.323 Hydrogen bonds: D:D.329, A:Y.325, B:D.329 NA.21: 5 residues within 4Å: Chain A: D.329 Chain B: Y.325 Chain C: D.329 Chain D: Y.325 Ligands: NA.7 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 1 interactions with chain C Water bridges: D:K.323, B:K.323 Hydrogen bonds: B:Y.325, B:Y.325, C:D.329 NA.28: 5 residues within 4Å: Chain A: Y.325 Chain B: D.329 Chain C: Y.325 Chain D: D.329 Ligands: NA.14 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:D.329, C:Y.325, A:Y.325 Water bridges: C:K.323, A:K.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neelon, K. et al., Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS. Biophys.J. (2011)

Release Date

2012-01-11

Peptides

Myo-inositol-1-phosphate synthase (Ino1): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Myo-inositol-1-phosphate synthase (Ino1)

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