SMTL ID : 3qvx.1

L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus mutant K367A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: T.228, G.229, E.230, T.231, K.278, K.306 Ligands: GOL.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.228, A:T.228, A:T.228, A:T.228, A:G.229, A:E.230, A:T.231, A:T.231 Salt bridges: A:K.278, A:K.306 PO4.11: 7 residues within 4Å: Chain B: T.228, G.229, E.230, T.231, K.278, K.306 Ligands: GOL.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.228, B:T.228, B:T.228, B:T.228, B:G.229, B:E.230, B:T.231, B:T.231 Salt bridges: B:K.278, B:K.306 PO4.21: 7 residues within 4Å: Chain C: T.228, G.229, E.230, T.231, K.278, K.306 Ligands: GOL.25 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.228, C:T.228, C:T.228, C:G.229, C:E.230, C:T.231 Salt bridges: C:K.278, C:K.306 PO4.31: 7 residues within 4Å: Chain D: T.228, G.229, E.230, T.231, K.278, K.306 Ligands: GOL.35 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.228, D:T.228, D:T.228, D:G.229, D:E.230, D:T.231 Salt bridges: D:K.278, D:K.306

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: D.174, R.175, K.176, E.177 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.174, A:K.176, A:E.177, A:E.177, A:E.177 Salt bridges: A:R.175 SO4.3: 4 residues within 4Å: Chain A: K.360, T.372, N.373, V.374 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.372, A:N.373, A:V.374 Water bridges: A:T.372 Salt bridges: A:K.360 SO4.12: 4 residues within 4Å: Chain B: D.174, R.175, K.176, E.177 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.174, B:K.176, B:E.177, B:E.177, B:E.177 Salt bridges: B:R.175 SO4.13: 4 residues within 4Å: Chain B: K.360, T.372, N.373, V.374 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.372, B:N.373, B:V.374 Water bridges: B:T.372 Salt bridges: B:K.360 SO4.22: 4 residues within 4Å: Chain C: D.174, R.175, K.176, E.177 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.174, C:K.176, C:E.177, C:E.177 Salt bridges: C:R.175 SO4.23: 4 residues within 4Å: Chain C: K.360, T.372, N.373, V.374 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.372, C:T.372, C:N.373, C:V.374 Salt bridges: C:K.360 SO4.32: 4 residues within 4Å: Chain D: D.174, R.175, K.176, E.177 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.174, D:K.176, D:E.177, D:E.177 Salt bridges: D:R.175 SO4.33: 4 residues within 4Å: Chain D: K.360, T.372, N.373, V.374 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.372, D:T.372, D:N.373, D:V.374 Salt bridges: D:K.360

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

NAD.4: 33 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, A.181, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336 Ligands: GOL.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.199, 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:T.99, A:A.148, A:S.149, A:Y.185, A:T.228, A:D.261, A:K.274 Water bridges: A:S.13, A:T.228, A:D.261, A:D.261, A:D.261, A:D.261, A:D.332 NAD.14: 33 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, A.181, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336 Ligands: GOL.15 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.199, 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:T.99, B:A.148, B:S.149, B:Y.185, B:T.228, B:D.261, B:K.274 Water bridges: B:S.13, B:T.228, B:D.261, B:D.261, B:D.261, B:D.261, B:D.332 NAD.24: 33 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, A.181, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336 Ligands: GOL.25 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:F.199, 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:T.99, C:A.148, C:S.149, C:T.150, C:T.228, C:T.228, C:D.261, C:K.274 Water bridges: C:S.13, C:T.150, C:T.150, C:E.151, C:D.261, C:D.261, C:D.261, C:D.261 NAD.34: 33 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, A.181, Y.185, F.199, T.200, D.225, G.226, T.228, Y.260, D.261, K.274, D.304, D.332, A.336 Ligands: GOL.35 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:F.199, 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:T.99, D:A.148, D:S.149, D:T.150, D:T.228, D:T.228, D:D.261, D:K.274 Water bridges: D:S.13, D:T.150, D:T.150, D:E.151, D:D.261, D:D.261, D:D.261, D:D.261

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: L.257, D.261, K.274, K.278, K.306, D.332 Ligands: PO4.1, NAD.4 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: K.263, Y.298, P.300 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: N.305, D.329, A.330, I.331 Chain B: K.323 Chain D: L.321, M.322, K.323 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: N.75, S.301, L.302, V.303, N.305, I.331 Chain B: H.313 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: L.257, D.261, K.274, K.278, K.306, D.332 Ligands: PO4.11, NAD.14 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: K.263, Y.298, P.300 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain A: K.323 Chain B: N.305, D.329, A.330, I.331 Chain C: L.321, M.322, K.323 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: H.313 Chain B: N.75, S.301, L.302, V.303, N.305, I.331 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain C: L.257, D.261, K.274, K.278, K.306, D.332 Ligands: PO4.21, NAD.24 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: K.263, Y.298, P.300 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain B: L.321, M.322, K.323 Chain C: N.305, D.329, A.330, I.331 Chain D: K.323 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: N.75, S.301, L.302, V.303, N.305, I.331 Chain D: H.313 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain D: L.257, D.261, K.274, K.278, K.306, D.332 Ligands: PO4.31, NAD.34 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain D: K.263, Y.298, P.300 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain A: L.321, M.322, K.323 Chain C: K.323 Chain D: N.305, D.329, A.330, I.331 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain C: H.313 Chain D: N.75, S.301, L.302, V.303, N.305, I.331 Ligand excluded by PLIP

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

PG4.9: 3 residues within 4Å: Chain A: E.131, E.132, K.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.131, A:E.132, A:K.135 PG4.19: 3 residues within 4Å: Chain B: E.131, E.132, K.135 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.131, B:E.132, B:K.135 PG4.29: 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 PG4.39: 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 NA: SODIUM ION(Non-functional Binders)

NA.10: 7 residues within 4Å: Chain A: D.329 Chain B: K.323, Y.325 Chain C: D.329 Chain D: K.323, Y.325 Ligands: NA.30 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.325, B:Y.325, C:D.329 NA.20: 7 residues within 4Å: Chain A: K.323, Y.325 Chain B: D.329 Chain C: K.323, Y.325 Chain D: D.329 Ligands: NA.40 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:D.329, A:Y.325, C:Y.325 NA.30: 7 residues within 4Å: Chain A: D.329 Chain B: K.323, Y.325 Chain C: D.329 Chain D: K.323, Y.325 Ligands: NA.10 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.329, B:Y.325, B:Y.325 NA.40: 7 residues within 4Å: Chain A: K.323, Y.325 Chain B: D.329 Chain C: K.323, Y.325 Chain D: D.329 Ligands: NA.20 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:Y.325, C:Y.325, D:D.329

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)