SMTL ID : 6kyi.1

Rice Rubisco in complex with sulfate ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-8-8-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.295, H.298, G.329, S.379 Chain C: N.123 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: K.175, G.381, G.403, G.404 Chain C: W.66 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain C: R.295, H.298, G.329 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain C: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain E: R.295, H.298, G.329, S.379 Chain G: N.123 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain E: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain E: K.175, G.381, G.403, G.404 Chain G: W.66 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain G: R.295, H.298, G.329 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain G: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain I: R.295, H.298, G.329, S.379 Chain K: N.123 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain I: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain I: K.175, G.381, G.403, G.404 Chain K: W.66 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain K: R.295, H.298, G.329 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain K: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain M: R.295, H.298, G.329, S.379 Chain O: N.123 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain M: R.134, K.305, H.310, M.341 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain M: K.175, G.381, G.403, G.404 Chain O: W.66 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain O: R.295, H.298, G.329 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain O: R.134, K.305, H.310, M.341 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.145, K.146, F.148, Q.149 Chain I: R.213 Chain K: E.110 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain I Hydrogen bonds: A:S.145, A:K.146, A:F.148 Water bridges: A:R.285, I:R.213, I:R.213 GOL.4: 4 residues within 4Å: Chain A: L.270, G.273 Chain C: L.270, M.297 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.270 GOL.10: 6 residues within 4Å: Chain E: S.145, K.146, F.148, Q.149 Chain M: R.213 Chain O: E.110 6 PLIP interactions: 2 interactions with chain M, 4 interactions with chain E Water bridges: M:R.213, M:R.213, E:R.285 Hydrogen bonds: E:S.145, E:K.146, E:F.148 GOL.11: 4 residues within 4Å: Chain E: L.270, G.273 Chain G: L.270, M.297 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:L.270 GOL.17: 6 residues within 4Å: Chain E: R.213 Chain G: E.110 Chain I: S.145, K.146, F.148, Q.149 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:S.145, I:K.146, I:F.148 Water bridges: I:R.285, E:R.213, E:R.213 GOL.18: 4 residues within 4Å: Chain I: L.270, G.273 Chain K: L.270, M.297 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:L.270 GOL.24: 6 residues within 4Å: Chain A: R.213 Chain C: E.110 Chain M: S.145, K.146, F.148, Q.149 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain M Water bridges: A:R.213, A:R.213, M:R.285 Hydrogen bonds: M:S.145, M:K.146, M:F.148 GOL.25: 4 residues within 4Å: Chain M: L.270, G.273 Chain O: L.270, M.297 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:L.270

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: ACEGIKMO
Ribulose bisphosphate carboxylase small chain, chloroplastic: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
A

G
B

I
A

K
B

M
A

O
B

B
S

D
T

F
S

H
T

J
S

L
T

N
S

P
T

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain, chloroplastic

Related Entries With Identical Sequence