SMTL ID : 5iu0.1

Rubisco from Arabidopsis thaliana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204 Chain B: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.11: 8 residues within 4Å: Chain A: N.123 Chain B: T.173, K.175, K.177, K.201, D.203, E.204 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.203, B:E.204

2 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.2: 22 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain B: E.60, T.65, W.66, N.123 Ligands: MG.1 33 PLIP interactions: 5 interactions with chain B, 28 interactions with chain A Hydrogen bonds: B:T.65, B:T.65, B:N.123, A:T.173, A:K.175, A:E.204, A:G.381, A:G.403, A:G.404 Water bridges: B:E.60, B:E.60, A:T.173, A:T.173, A:K.177, A:K.177, A:R.295, A:R.295, A:H.327, A:H.327, A:G.329, A:S.379, A:S.379, A:G.380, A:G.380, A:I.382, A:G.405 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.12: 23 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain B: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.11 32 PLIP interactions: 28 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.173, B:T.173, B:K.175, B:G.381, B:G.403, B:G.404, A:T.65, A:N.123 Water bridges: B:T.173, B:T.173, B:K.177, B:K.177, B:H.294, B:R.295, B:R.295, B:R.295, B:H.327, B:G.329, B:S.379, B:I.382, B:I.382, B:I.382, B:Q.401, A:T.65, A:T.65 Salt bridges: B:K.175, B:K.175, B:K.177, B:R.295, B:H.327, B:K.334, B:K.334

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

EDO.3: 6 residues within 4Å: Chain A: G.111, F.148, Q.149, T.278, H.282 Chain B: T.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.149 Water bridges: A:G.111 EDO.4: 4 residues within 4Å: Chain A: T.145, K.146, F.148, L.371 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.146, A:K.146 EDO.5: 2 residues within 4Å: Chain A: E.110 Chain B: R.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.110 EDO.6: 9 residues within 4Å: Chain A: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.16, A:K.18, A:T.68 Water bridges: A:K.18, A:Y.20 EDO.7: 3 residues within 4Å: Chain A: L.270 Chain B: L.270, M.297 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: Q.304, N.306, H.307 Chain B: Q.304, N.306, H.307 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.306, B:H.307, A:N.306, A:N.306 EDO.9: 7 residues within 4Å: Chain A: G.64, T.65, T.67, T.68, V.69, D.72 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.65, A:T.65, A:D.72 Water bridges: A:K.18 EDO.10: 3 residues within 4Å: Chain A: Q.149, H.282, D.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.286 Water bridges: A:R.285 EDO.13: 9 residues within 4Å: Chain B: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.16, B:K.18 Water bridges: B:E.19, B:Y.20 EDO.14: 8 residues within 4Å: Chain B: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.24, B:Y.24, B:T.67, B:V.69 Water bridges: B:T.65, B:T.65 EDO.15: 5 residues within 4Å: Chain B: N.163, Y.165 Chain C: E.68, R.155, S.169 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.169 Water bridges: C:R.155, C:R.155, C:S.169 EDO.16: 5 residues within 4Å: Chain A: N.163, Y.165 Chain D: E.68, R.155, S.169 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.166, D:S.169, A:Y.165 Water bridges: D:R.155, D:S.169, A:Y.165 EDO.17: 5 residues within 4Å: Chain A: D.160, N.163, Y.165 Chain D: R.120, Y.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.160, A:Y.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valegard, K. et al., Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate. Acta Crystallogr D Struct Biol (2018)

Release Date

2017-07-12

Peptides

Ribulose bisphosphate carboxylase large chain: AB
Ribulose bisphosphate carboxylase small chain 1B, chloroplastic: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
J

D
I

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain 1B, chloroplastic