SMTL ID : 6mgi.1

Photosynthetic phosphoenolpyruvate carboxylase isoenzyme from maize complexed with the allosteric activator glucose-6-phosphate in its allosteric site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-tetramer

Ligands

4 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: L.97, S.100, F.225, R.226, T.227, E.229 Chain B: W.333, R.334 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.100, A:E.229, B:W.333, G.1 Salt bridges: A:R.226, B:R.334 GLY.8: 9 residues within 4Å: Chain A: W.333, R.334 Chain B: S.100, F.225, R.226, T.227, D.228, E.229, L.938 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: A:R.334 Hydrogen bonds: B:S.100, B:S.100, B:D.228, G.8 GLY.15: 8 residues within 4Å: Chain C: L.97, S.100, F.225, R.226, T.227, E.229 Chain D: W.333, R.334 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:S.100, C:E.229, D:W.333, G.15 Salt bridges: C:R.226, D:R.334 GLY.22: 9 residues within 4Å: Chain C: W.333, R.334 Chain D: S.100, F.225, R.226, T.227, D.228, E.229, L.938 6 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: G.22, D:S.100, D:S.100, D:D.228, D:D.228 Salt bridges: C:R.334

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.2: 10 residues within 4Å: Chain A: R.183, R.184, S.185, R.231, D.239 Chain B: E.360, F.361, W.362, K.363, R.372 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.360, B:F.361, B:W.362, B:K.363, B:K.363, A:R.184, A:S.185 Salt bridges: A:R.183, A:R.184, A:R.231 G6P.9: 10 residues within 4Å: Chain A: E.360, F.361, W.362, K.363, R.372 Chain B: R.183, R.184, S.185, R.231, D.239 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.184, B:S.185, B:D.239, A:F.361, A:K.363 Salt bridges: B:R.183, B:R.184, B:R.231 G6P.16: 10 residues within 4Å: Chain C: R.183, R.184, S.185, R.231, D.239 Chain D: E.360, F.361, W.362, K.363, R.372 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:F.361, D:W.362, D:K.363, D:K.363, C:R.184, C:S.185 Salt bridges: C:R.183, C:R.184, C:R.231 G6P.23: 10 residues within 4Å: Chain C: E.360, F.361, W.362, K.363, R.372 Chain D: R.183, R.184, S.185, R.231, D.239 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:E.360, C:F.361, C:K.363, D:R.184, D:S.185, D:D.239 Salt bridges: D:R.183, D:R.184, D:R.231

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: R.610, A.614, R.641, S.658, T.825 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.610, A:R.641, A:S.658, A:T.825 EDO.4: 8 residues within 4Å: Chain A: Y.601, A.614, L.617, Q.621, S.658, Q.659, F.821 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.601, A:Q.621, A:Q.621 EDO.5: 5 residues within 4Å: Chain A: Q.180, R.231, E.240, Y.243, I.756 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.231, A:R.231 EDO.6: 7 residues within 4Å: Chain A: T.644, V.645, G.646, V.790, M.831, V.832, N.968 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.645, A:G.646, A:K.835 Water bridges: A:T.782, A:H.787 EDO.10: 9 residues within 4Å: Chain B: Y.601, R.610, A.614, Q.621, R.641, S.658, Q.659, P.660 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.610, B:A.614, B:Q.621, B:Q.621 EDO.11: 8 residues within 4Å: Chain B: R.610, A.614, R.641, A.655, S.658, T.825, L.828 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.610, B:R.610, B:R.641, B:S.658, B:S.658 EDO.17: 6 residues within 4Å: Chain C: R.610, A.614, R.641, S.658, T.825 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.610, C:R.641, C:S.658, C:T.825 EDO.18: 8 residues within 4Å: Chain C: Y.601, A.614, L.617, Q.621, S.658, Q.659, F.821 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.621, C:Q.621 EDO.19: 5 residues within 4Å: Chain C: Q.180, R.231, E.240, Y.243, I.756 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.231, C:R.231 EDO.20: 7 residues within 4Å: Chain C: T.644, V.645, G.646, V.790, M.831, V.832, N.968 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.645, C:G.646, C:K.835 Water bridges: C:T.782, C:H.787 EDO.24: 9 residues within 4Å: Chain D: Y.601, R.610, A.614, Q.621, R.641, S.658, Q.659, P.660 Ligands: EDO.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.610, D:A.614, D:Q.621, D:Q.621 EDO.25: 8 residues within 4Å: Chain D: R.610, A.614, R.641, A.655, S.658, T.825, L.828 Ligands: EDO.24 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.610, D:R.610, D:R.641, D:S.658, D:S.658

4 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.7: 10 residues within 4Å: Chain A: H.177, R.456, E.566, M.598, Y.601, S.602, D.603, G.640, Q.673, R.773 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.601, A:S.602, A:S.602, A:S.602, A:D.603, A:Q.673 Salt bridges: A:H.177, A:R.456, A:R.773 PGA.14: 12 residues within 4Å: Chain B: H.177, R.456, E.566, M.598, G.600, Y.601, S.602, D.603, G.640, Q.673, R.773, I.775 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.601, B:S.602, B:S.602, B:S.602, B:D.603, B:Q.673 Salt bridges: B:H.177, B:H.177, B:R.456, B:R.773 PGA.21: 10 residues within 4Å: Chain C: H.177, R.456, E.566, M.598, Y.601, S.602, D.603, G.640, Q.673, R.773 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.566, C:Y.601, C:S.602, C:S.602, C:S.602, C:D.603, C:Q.673 Salt bridges: C:H.177, C:R.456, C:R.773 PGA.28: 12 residues within 4Å: Chain D: H.177, R.456, E.566, M.598, G.600, Y.601, S.602, D.603, G.640, Q.673, R.773, I.775 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:E.566, D:Y.601, D:S.602, D:S.602, D:S.602, D:D.603, D:Q.673 Salt bridges: D:H.177, D:H.177, D:R.456, D:R.773

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 10 residues within 4Å: Chain A: R.192, R.219, E.220, A.223 Chain B: E.329, L.330, I.431, G.434, S.435, L.436 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.435, B:L.436, A:R.192, A:E.220 GOL.13: 6 residues within 4Å: Chain A: A.216, R.219 Chain B: R.261, G.434, S.435, D.438 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.438, A:R.219 GOL.26: 10 residues within 4Å: Chain C: R.192, R.219, E.220, A.223 Chain D: E.329, L.330, I.431, G.434, S.435, L.436 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.329, D:S.435, D:L.436, C:R.192 GOL.27: 6 residues within 4Å: Chain C: A.216, R.219 Chain D: R.261, G.434, S.435, D.438 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.438, C:R.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munoz-Clares, R.A. et al., Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C4-phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics. Biochem.J. (2020)

Release Date

2019-09-18

Peptides

Phosphoenolpyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Phosphoenolpyruvate carboxylase

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