SMTL ID : 8oje.2 (1 other biounit)

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 in complex with L-malate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

homo-tetramer

Ligands

4 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.1: 11 residues within 4Å: Chain A: R.650, G.651, P.654, Q.682, M.834, K.838, L.890, L.894, R.897, Q.971, N.972 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.890 Hydrogen bonds: A:G.651, A:Q.682, A:L.970, A:N.972, A:N.972 Salt bridges: A:R.650, A:K.838, A:R.897 LMR.12: 11 residues within 4Å: Chain B: R.650, G.651, P.654, Q.682, M.834, K.838, L.890, R.897, L.970, Q.971, N.972 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.651, B:Q.682, B:N.972, B:N.972 Salt bridges: B:R.650, B:K.838, B:R.897 LMR.21: 10 residues within 4Å: Chain C: R.650, G.651, P.654, Q.682, M.834, K.838, L.890, R.897, Q.971, N.972 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.651, C:Q.682, C:N.972 Salt bridges: C:R.650, C:K.838, C:R.897 LMR.31: 12 residues within 4Å: Chain D: R.650, G.651, P.654, Q.682, M.834, K.838, L.890, L.894, R.897, L.970, Q.971, N.972 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.651, D:Q.682, D:N.972 Salt bridges: D:R.650, D:K.838, D:R.897

20 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: G.437, S.438 Ligands: PEG.3 Ligand excluded by PLIP PEG.3: 5 residues within 4Å: Chain A: E.332, G.437, S.438 Chain B: E.223 Ligands: PEG.2 Ligand excluded by PLIP PEG.4: 2 residues within 4Å: Ligands: PEG.5, PEG.13 Ligand excluded by PLIP PEG.5: 6 residues within 4Å: Chain A: H.252, W.256, K.257, N.324, Q.325 Ligands: PEG.4 Ligand excluded by PLIP PEG.6: 2 residues within 4Å: Chain A: L.216 Ligands: PEG.16 Ligand excluded by PLIP PEG.7: 4 residues within 4Å: Chain A: L.203, Y.204, K.213, D.217 Ligand excluded by PLIP PEG.13: 4 residues within 4Å: Chain B: W.256, N.324, Q.325 Ligands: PEG.4 Ligand excluded by PLIP PEG.14: 5 residues within 4Å: Chain B: L.203, Y.204, K.213, D.217 Ligands: PEG.15 Ligand excluded by PLIP PEG.15: 2 residues within 4Å: Chain B: K.213 Ligands: PEG.14 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain A: R.195, A.219, E.223 Chain B: S.438 Ligands: PEG.6 Ligand excluded by PLIP PEG.22: 3 residues within 4Å: Chain C: G.437, S.438 Ligands: PEG.23 Ligand excluded by PLIP PEG.23: 5 residues within 4Å: Chain C: E.332, G.437, S.438 Chain D: E.223 Ligands: PEG.22 Ligand excluded by PLIP PEG.24: 3 residues within 4Å: Chain C: N.324 Ligands: PEG.25, PEG.32 Ligand excluded by PLIP PEG.25: 5 residues within 4Å: Chain C: H.252, W.256, N.324, Q.325 Ligands: PEG.24 Ligand excluded by PLIP PEG.26: 4 residues within 4Å: Chain C: A.219, E.223 Chain D: S.438 Ligands: PEG.27 Ligand excluded by PLIP PEG.27: 2 residues within 4Å: Chain C: L.216 Ligands: PEG.26 Ligand excluded by PLIP PEG.28: 4 residues within 4Å: Chain C: L.203, Y.204, K.213, D.217 Ligand excluded by PLIP PEG.32: 3 residues within 4Å: Chain D: N.324, Q.325 Ligands: PEG.24 Ligand excluded by PLIP PEG.33: 5 residues within 4Å: Chain D: L.203, Y.204, K.213, D.217 Ligands: PEG.34 Ligand excluded by PLIP PEG.34: 2 residues within 4Å: Chain D: K.213 Ligands: PEG.33 Ligand excluded by PLIP

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

CL.8: 5 residues within 4Å: Chain A: D.665, T.666, I.667, N.668, H.704 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Q.241, R.245 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: Y.204 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.391 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: D.665, I.667, N.668, H.704 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: Q.241, R.245 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: R.186, S.188 Chain B: W.365, R.375 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: W.365, R.375 Chain B: R.186, R.187, S.188 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: D.665, I.667, N.668, H.704 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: Q.241, R.245 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain D: D.665, I.667, N.668, H.704 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain D: R.245 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, T.J. et al., Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants. To Be Published

Release Date

2023-05-31

Peptides

Phosphoenolpyruvate carboxylase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
G

D
H

Phosphoenolpyruvate carboxylase 1

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