SMTL ID : 6kyj.1 (2 other biounits)

Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.380, G.381, G.403, G.404 Chain C: W.66 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.381, A:I.382, A:G.403, A:G.404 Water bridges: A:G.380, A:G.380, A:G.405 SO4.2: 4 residues within 4Å: Chain A: R.295, H.298, G.329 Chain C: N.123 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Water bridges: A:H.327, A:G.329, A:S.379, A:S.379 Salt bridges: A:R.295, A:H.298 Hydrogen bonds: C:N.123 SO4.3: 4 residues within 4Å: Chain A: R.134, K.305, H.310, M.341 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.312 Salt bridges: A:R.134, A:K.305, A:H.310 SO4.4: 3 residues within 4Å: Chain A: T.26, K.81, R.83 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.81, A:R.83 SO4.5: 2 residues within 4Å: Chain A: N.442, R.446 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.442 Water bridges: A:N.442, A:E.443 Salt bridges: A:R.446 SO4.6: 3 residues within 4Å: Chain A: K.356, F.364, T.365 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.365, A:T.365 Water bridges: A:K.356, A:K.356 Salt bridges: A:K.356 SO4.10: 5 residues within 4Å: Chain A: W.66 Chain C: G.380, G.381, G.403, G.404 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.381, C:I.382, C:G.403, C:G.404 Water bridges: C:G.380, C:G.380, C:G.405 SO4.11: 4 residues within 4Å: Chain A: N.123 Chain C: R.295, H.298, G.329 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Water bridges: C:G.329, C:S.379, C:S.379, C:S.379 Salt bridges: C:R.295, C:H.298 Hydrogen bonds: A:N.123 SO4.12: 4 residues within 4Å: Chain C: R.134, K.305, H.310, M.341 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.312 Salt bridges: C:R.134, C:K.305, C:H.310 SO4.13: 3 residues within 4Å: Chain C: T.26, K.81, R.83 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.81, C:R.83 SO4.14: 2 residues within 4Å: Chain C: N.442, R.446 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.442 Water bridges: C:N.442, C:E.443 Salt bridges: C:R.446 SO4.15: 3 residues within 4Å: Chain C: K.356, F.364, T.365 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.365 Water bridges: C:K.356, C:K.356 Salt bridges: C:K.356

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: S.145, K.146, F.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.145, A:K.146, A:F.148 Water bridges: A:R.285 GOL.8: 5 residues within 4Å: Chain A: Y.190, K.227, E.231 Chain B: A.52, Y.53 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.190, A:K.227, A:K.227, B:A.52 GOL.9: 4 residues within 4Å: Chain A: A.430, E.433, R.435 Chain B: Q.71 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.433, A:R.435, B:Q.71 Water bridges: A:A.430 GOL.16: 3 residues within 4Å: Chain C: S.145, K.146, F.148 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.145, C:K.146, C:F.148 Water bridges: C:R.285 GOL.17: 5 residues within 4Å: Chain C: Y.190, K.227, E.231 Chain D: A.52, Y.53 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.52, C:K.227, C:K.227, C:E.231 GOL.18: 4 residues within 4Å: Chain C: A.430, E.433, R.435 Chain D: Q.71 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.71, C:E.433, C:R.435 Water bridges: C:A.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumura, H. et al., Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C 4 Plant-like High Catalytic Activity. Mol Plant (2020)

Release Date

2020-09-16

Peptides

Ribulose bisphosphate carboxylase large chain: AC
Ribulose bisphosphate carboxylase small chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
S

D
S

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain

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