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

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 G678S mutant with bound malate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-tetramer

Ligands

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

LMR.1: 10 residues within 4Å: Chain A: R.650, G.651, P.654, Q.682, M.834, K.838, L.894, R.897, Q.971, N.972 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.651, A:Q.682, A:N.972 Water bridges: A:G.651 Salt bridges: A:R.650, A:K.838, A:R.897 LMR.13: 10 residues within 4Å: Chain B: R.650, G.651, P.654, Q.682, M.834, K.838, L.894, R.897, Q.971, N.972 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.651, B:Q.682, B:N.972 Water bridges: B:G.651 Salt bridges: B:R.650, B:K.838, B:R.897 LMR.25: 10 residues within 4Å: Chain C: R.650, G.651, P.654, Q.682, M.834, K.838, L.894, R.897, Q.971, N.972 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.651, C:Q.682, C:N.972 Water bridges: C:G.651 Salt bridges: C:R.650, C:K.838, C:R.897 LMR.37: 10 residues within 4Å: Chain D: R.650, G.651, P.654, Q.682, M.834, K.838, L.894, R.897, Q.971, N.972 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.651, D:Q.682, D:N.972 Water bridges: D:G.651 Salt bridges: D:R.650, D:K.838, D:R.897

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

CL.2: 4 residues within 4Å: Chain A: R.264, R.278 Chain D: E.218, R.222 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: Q.241, R.245, D.309 Chain D: K.366 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: D.665, T.666, I.667, N.668, H.704 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.186, S.188 Chain D: W.365, R.375 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: R.264, R.278 Chain C: E.218, R.222 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: Q.241, R.245, D.309 Chain C: K.366 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: D.665, T.666, I.667, N.668, H.704 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: R.186, S.188 Chain C: W.365, R.375 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain B: E.218, R.222 Chain C: R.264, R.278 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: K.366 Chain C: Q.241, R.245, D.309 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain C: D.665, T.666, I.667, N.668, H.704 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: W.365, R.375 Chain C: R.186, S.188 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain A: E.218, R.222 Chain D: R.264, R.278 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain A: K.366 Chain D: Q.241, R.245, D.309 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain D: D.665, T.666, I.667, N.668, H.704 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain A: W.365, R.375 Chain D: R.186, S.188 Ligand excluded by PLIP

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

PEG.6: 4 residues within 4Å: Chain D: K.257, N.324, Q.325 Ligands: PEG.7 Ligand excluded by PLIP PEG.7: 3 residues within 4Å: Chain D: N.324 Ligands: PEG.6, PEG.43 Ligand excluded by PLIP PEG.8: 4 residues within 4Å: Chain A: L.203, Y.204, K.213 Ligands: PEG.9 Ligand excluded by PLIP PEG.9: 2 residues within 4Å: Chain A: K.213 Ligands: PEG.8 Ligand excluded by PLIP PEG.10: 3 residues within 4Å: Chain A: E.487, Q.490, R.583 Ligand excluded by PLIP PEG.11: 1 residues within 4Å: Ligands: PEG.12 Ligand excluded by PLIP PEG.12: 1 residues within 4Å: Ligands: PEG.11 Ligand excluded by PLIP PEG.18: 4 residues within 4Å: Chain C: K.257, N.324, Q.325 Ligands: PEG.19 Ligand excluded by PLIP PEG.19: 3 residues within 4Å: Chain C: N.324 Ligands: PEG.18, PEG.31 Ligand excluded by PLIP PEG.20: 4 residues within 4Å: Chain B: L.203, Y.204, K.213 Ligands: PEG.21 Ligand excluded by PLIP PEG.21: 2 residues within 4Å: Chain B: K.213 Ligands: PEG.20 Ligand excluded by PLIP PEG.22: 3 residues within 4Å: Chain B: E.487, Q.490, R.583 Ligand excluded by PLIP PEG.23: 1 residues within 4Å: Ligands: PEG.24 Ligand excluded by PLIP PEG.24: 1 residues within 4Å: Ligands: PEG.23 Ligand excluded by PLIP PEG.30: 4 residues within 4Å: Chain B: K.257, N.324, Q.325 Ligands: PEG.31 Ligand excluded by PLIP PEG.31: 3 residues within 4Å: Chain B: N.324 Ligands: PEG.19, PEG.30 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain C: L.203, Y.204, K.213 Ligands: PEG.33 Ligand excluded by PLIP PEG.33: 2 residues within 4Å: Chain C: K.213 Ligands: PEG.32 Ligand excluded by PLIP PEG.34: 3 residues within 4Å: Chain C: E.487, Q.490, R.583 Ligand excluded by PLIP PEG.35: 1 residues within 4Å: Ligands: PEG.36 Ligand excluded by PLIP PEG.36: 1 residues within 4Å: Ligands: PEG.35 Ligand excluded by PLIP PEG.42: 4 residues within 4Å: Chain A: K.257, N.324, Q.325 Ligands: PEG.43 Ligand excluded by PLIP PEG.43: 3 residues within 4Å: Chain A: N.324 Ligands: PEG.7, PEG.42 Ligand excluded by PLIP PEG.44: 4 residues within 4Å: Chain D: L.203, Y.204, K.213 Ligands: PEG.45 Ligand excluded by PLIP PEG.45: 2 residues within 4Å: Chain D: K.213 Ligands: PEG.44 Ligand excluded by PLIP PEG.46: 3 residues within 4Å: Chain D: E.487, Q.490, R.583 Ligand excluded by PLIP PEG.47: 1 residues within 4Å: Ligands: PEG.48 Ligand excluded by PLIP PEG.48: 1 residues within 4Å: Ligands: PEG.47 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

2024-10-23

Peptides

Phosphoenolpyruvate carboxylase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

D
C

Phosphoenolpyruvate carboxylase 1

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