SMTL ID : 3zgb.1

Greater efficiency of photosynthetic carbon fixation due to single amino acid substitution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 8 residues within 4Å: Chain A: R.647, Q.679, M.831, K.835, L.887, R.890, R.894, N.970 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Q.679, A:Q.679, A:N.970, D.1 Salt bridges: A:R.647, A:K.835, A:R.890, A:R.894 ASP.5: 9 residues within 4Å: Chain B: R.647, Q.679, M.831, K.835, L.887, R.890, R.894, Q.969, N.970 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:Q.679, B:Q.679, B:N.970, B:N.970, D.5, D.5 Salt bridges: B:R.647, B:K.835, B:R.890, B:R.894 ASP.9: 8 residues within 4Å: Chain C: R.647, Q.679, M.831, K.835, L.887, R.890, R.894, N.970 8 PLIP interactions: 7 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:Q.679, C:Q.679, C:N.970, D.9 Salt bridges: C:R.647, C:K.835, C:R.890, C:R.894 ASP.13: 9 residues within 4Å: Chain D: R.647, Q.679, M.831, K.835, L.887, R.890, R.894, Q.969, N.970 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:Q.679, D:Q.679, D:N.970, D:N.970, D.13, D.13 Salt bridges: D:R.647, D:K.835, D:R.890, D:R.894

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

EDO.2: 9 residues within 4Å: Chain A: G.642, G.643, G.646, R.647, Q.673, L.828, N.970, T.971, G.972 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.673, A:N.970, A:T.971, A:G.972, A:G.972 EDO.6: 8 residues within 4Å: Chain B: G.642, G.643, R.647, Q.673, L.828, N.970, T.971, G.972 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.673, B:Q.673, B:N.970, B:T.971 EDO.10: 9 residues within 4Å: Chain C: G.642, G.643, G.646, R.647, Q.673, L.828, N.970, T.971, G.972 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.673, C:N.970, C:T.971, C:G.972, C:G.972 EDO.14: 8 residues within 4Å: Chain D: G.642, G.643, R.647, Q.673, L.828, N.970, T.971, G.972 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.673, D:Q.673, D:N.970, D:T.971

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

SO4.3: 5 residues within 4Å: Chain A: R.184, R.185, S.186 Chain C: E.369, R.372 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.369, A:S.186 Salt bridges: C:R.372, A:R.184 SO4.4: 6 residues within 4Å: Chain A: R.456, D.603, R.641, R.773, A.774, I.775 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.774, A:I.775 Salt bridges: A:R.456, A:R.773 SO4.7: 4 residues within 4Å: Chain B: R.184, R.185, S.186 Chain D: R.372 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.185, B:S.186 Salt bridges: B:R.184, D:R.372 SO4.8: 6 residues within 4Å: Chain B: R.456, D.603, R.641, R.773, A.774, I.775 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.603, B:A.774, B:I.775 Salt bridges: B:R.456, B:R.773 SO4.11: 5 residues within 4Å: Chain A: E.369, R.372 Chain C: R.184, R.185, S.186 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.369, C:S.186 Salt bridges: A:R.372, C:R.184 SO4.12: 6 residues within 4Å: Chain C: R.456, D.603, R.641, R.773, A.774, I.775 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.774, C:I.775 Salt bridges: C:R.456, C:R.773 SO4.15: 4 residues within 4Å: Chain B: R.372 Chain D: R.184, R.185, S.186 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.185, D:S.186 Salt bridges: D:R.184, B:R.372 SO4.16: 6 residues within 4Å: Chain D: R.456, D.603, R.641, R.773, A.774, I.775 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.603, D:A.774, D:I.775 Salt bridges: D:R.456, D:R.773

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paulus, J.K. et al., Greater Efficiency of Photosynthetic Carbon Fixation due to Single Amino Acid Substitution. Nat.Commun. (2013)

Release Date

2013-02-27

Peptides

PHOSPHOENOLPYRUVATE CARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PHOSPHOENOLPYRUVATE CARBOXYLASE