SMTL ID : 3s28.2 (1 other biounit)

The crystal structure of sucrose synthase-1 in complex with a breakdown product of the UDP-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 23 residues within 4Å: Chain A: L.296, G.297, G.302, G.303, Q.304, V.306, Y.533, M.578, A.579, R.580, K.585, V.609, S.647, Q.648, M.649, N.654, E.675, G.678, L.679, T.680, E.683 Ligands: LCN.2, NHF.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.303, A:Q.304, A:Q.648, A:Q.648, A:N.654, A:L.679, A:T.680, A:E.683 Salt bridges: A:R.580, A:K.585, A:K.585 UDP.9: 22 residues within 4Å: Chain B: L.296, G.297, G.302, G.303, V.306, Y.533, M.578, A.579, R.580, K.585, V.609, S.647, Q.648, M.649, N.654, E.675, G.678, L.679, T.680, E.683 Ligands: LCN.10, NHF.16 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.303, B:Q.304, B:Q.648, B:Q.648, B:N.654, B:G.678, B:L.679, B:T.680, B:E.683 Water bridges: B:Y.533, B:Y.533, B:R.580, B:R.580, B:Q.670 Salt bridges: B:R.580, B:K.585, B:K.585 UDP.17: 23 residues within 4Å: Chain C: L.296, G.297, G.302, G.303, V.306, Y.533, M.578, A.579, R.580, K.585, V.609, S.647, Q.648, M.649, N.654, Y.658, E.675, G.678, L.679, T.680, E.683 Ligands: LCN.18, NHF.24 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.303, C:Y.533, C:Q.648, C:Q.648, C:N.654, C:E.675, C:G.678, C:L.679, C:T.680, C:E.683 Water bridges: C:R.580, C:R.580, C:Q.670 Salt bridges: C:R.580, C:K.585, C:K.585 UDP.25: 20 residues within 4Å: Chain D: L.296, G.302, G.303, V.306, Y.533, M.578, A.579, R.580, K.585, V.609, S.647, Q.648, N.654, E.675, G.678, L.679, T.680, E.683 Ligands: LCN.26, NHF.32 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.303, D:Q.304, D:Q.648, D:Q.648, D:N.654, D:Y.658, D:E.675, D:G.678, D:L.679, D:T.680, D:E.683 Salt bridges: D:R.580, D:K.585, D:K.585

4 x LCN: 1,5-anhydro-D-arabino-hex-1-enitol(Non-covalent)

LCN.2: 12 residues within 4Å: Chain A: G.303, Q.304, Y.307, H.438, A.439, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.1, NHF.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.438, A:E.675, A:E.675, A:A.676, A:F.677, A:G.678, A:L.679 LCN.10: 13 residues within 4Å: Chain B: G.303, Q.304, Y.307, H.438, A.439, R.580, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.9, NHF.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.438, B:E.675, B:A.676, B:F.677, B:G.678, B:L.679 Water bridges: B:S.481 LCN.18: 12 residues within 4Å: Chain C: G.303, Q.304, Y.307, H.438, A.439, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.17, NHF.24 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.438, C:E.675, C:E.675, C:A.676, C:F.677, C:G.678, C:L.679 LCN.26: 12 residues within 4Å: Chain D: G.303, Q.304, Y.307, H.438, R.580, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.25, NHF.32 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.438, D:A.676, D:F.677, D:G.678, D:L.679

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

SO4.3: 3 residues within 4Å: Chain A: G.350, E.351, R.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.352 SO4.4: 4 residues within 4Å: Chain A: I.703, V.704, H.705, H.711 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.705 Salt bridges: A:H.711 SO4.5: 4 residues within 4Å: Chain A: H.716, G.717, D.718, Q.719 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.717, A:D.718, A:Q.719, A:Q.719 Salt bridges: A:H.716 SO4.11: 4 residues within 4Å: Chain B: G.350, E.351, R.352, L.353 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.352, B:L.353 SO4.12: 5 residues within 4Å: Chain B: A.700, I.703, V.704, H.705, H.711 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.705 Salt bridges: B:H.711 SO4.13: 4 residues within 4Å: Chain B: H.716, G.717, D.718, Q.719 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.717, B:D.718, B:Q.719, B:Q.719 Salt bridges: B:H.716 SO4.19: 3 residues within 4Å: Chain C: G.350, E.351, R.352 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.352 SO4.20: 4 residues within 4Å: Chain C: I.703, V.704, H.705, H.711 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.705 Salt bridges: C:H.711 SO4.21: 4 residues within 4Å: Chain C: H.716, G.717, D.718, Q.719 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.717, C:D.718, C:Q.719, C:Q.719 Salt bridges: C:H.716 SO4.27: 3 residues within 4Å: Chain D: G.350, E.351, R.352 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.352 SO4.28: 5 residues within 4Å: Chain D: A.700, I.703, V.704, H.705, H.711 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.703, D:H.705 Salt bridges: D:H.711 SO4.29: 4 residues within 4Å: Chain D: H.716, G.717, D.718, Q.719 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.717, D:D.718, D:D.718, D:D.718, D:Q.719, D:Q.719 Salt bridges: D:H.716

4 x MLA: MALONIC ACID(Non-covalent)

MLA.6: 6 residues within 4Å: Chain A: F.710, T.723, D.726, F.727, K.730, H.737 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.730 Hydrogen bonds: A:D.726 Salt bridges: A:K.730, A:K.730, A:H.737 MLA.14: 6 residues within 4Å: Chain B: F.710, T.723, D.726, F.727, K.730, H.737 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.727 Salt bridges: B:K.730, B:K.730, B:H.737 MLA.22: 6 residues within 4Å: Chain C: F.710, T.723, D.726, F.727, K.730, H.737 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.710 Salt bridges: C:K.730, C:K.730, C:H.737 MLA.30: 6 residues within 4Å: Chain D: F.710, T.723, D.726, F.727, K.730, H.737 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.710 Salt bridges: D:K.730, D:K.730, D:H.737

4 x NHF: 1,5-anhydro-D-fructose(Non-covalent)

NHF.7: 12 residues within 4Å: Chain A: G.303, Q.304, Y.307, H.438, A.439, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.1, LCN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.675, A:E.675, A:A.676, A:F.677, A:G.678, A:L.679 NHF.16: 12 residues within 4Å: Chain B: G.303, Q.304, Y.307, H.438, A.439, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.9, LCN.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.438, B:E.675, B:A.676, B:F.677, B:G.678, B:L.679 Water bridges: B:S.481 NHF.24: 13 residues within 4Å: Chain C: G.303, Q.304, Y.307, H.438, A.439, S.481, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.17, LCN.18 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.481, C:S.481, C:E.675, C:E.675, C:A.676, C:F.677, C:G.678, C:L.679 NHF.32: 12 residues within 4Å: Chain D: G.303, Q.304, Y.307, H.438, A.439, E.675, A.676, F.677, G.678, L.679 Ligands: UDP.25, LCN.26 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.438, D:A.676, D:F.677, D:G.678

4 x K: POTASSIUM ION(Non-covalent)

K.8: 7 residues within 4Å: Chain A: L.184, R.185, L.186, H.187, N.193, L.194, L.196 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.184, A:R.185, A:L.194, A:L.196 K.15: 6 residues within 4Å: Chain B: L.184, R.185, H.187, N.193, L.194, L.196 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:L.184, B:R.185, B:H.187, B:L.194, B:L.196 K.23: 7 residues within 4Å: Chain C: L.184, R.185, L.186, H.187, N.193, L.194, L.196 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.184, C:R.185, C:H.187, C:L.194, C:L.196 K.31: 7 residues within 4Å: Chain D: L.184, R.185, L.186, H.187, N.193, L.194, L.196 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:R.185, D:H.187, D:L.194, D:L.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Y. et al., The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications. J.Biol.Chem. (2011)

Release Date

2011-08-24

Peptides

Sucrose synthase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Sucrose synthase 1

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