SMTL ID : 7t1j.1 (1 other biounit)

Crystal structure of RUBISCO from Rhodospirillaceae bacterium BRH_c57

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-hexamer

Ligands

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

CAP.1: 24 residues within 4Å: Chain A: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, S.392, G.393, G.394 Chain B: E.48, T.53, N.111 Ligands: MG.2 31 PLIP interactions: 29 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.166, A:E.194, A:H.287, A:S.368, A:G.370, A:G.393, A:G.394, B:T.53, B:N.111 Water bridges: A:K.168, A:K.168, A:K.168, A:H.291, A:H.291, A:H.291, A:H.291, A:H.321, A:K.329, A:S.368, A:S.368, A:S.368, A:M.371, A:M.371, A:G.395 Salt bridges: A:K.166, A:K.166, A:K.168, A:R.288, A:H.321, A:K.329, A:K.329 CAP.3: 24 residues within 4Å: Chain A: E.48, T.53, N.111 Chain B: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, S.392, G.393, G.394 Ligands: MG.4 29 PLIP interactions: 27 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.166, B:E.194, B:H.287, B:S.368, B:G.370, B:G.393, B:G.394, A:T.53, A:N.111 Water bridges: B:K.168, B:K.168, B:K.168, B:K.168, B:R.288, B:H.291, B:H.291, B:H.291, B:H.321, B:G.323, B:G.369, B:M.371, B:G.395 Salt bridges: B:K.166, B:K.166, B:K.168, B:R.288, B:H.321, B:K.329, B:K.329 CAP.5: 24 residues within 4Å: Chain C: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, S.392, G.393, G.394 Chain D: E.48, T.53, N.111 Ligands: MG.6 26 PLIP interactions: 25 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.166, C:E.194, C:H.287, C:H.291, C:S.368, C:G.370, C:T.391, C:G.393, C:G.394, D:N.111 Water bridges: C:K.168, C:K.168, C:R.288, C:R.288, C:H.321, C:K.329, C:S.368, C:M.371, C:G.395 Salt bridges: C:K.166, C:K.166, C:K.168, C:R.288, C:H.321, C:K.329, C:K.329 CAP.7: 25 residues within 4Å: Chain C: E.48, T.53, N.54, N.111 Chain D: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, S.392, G.393, G.394 Ligands: MG.8 31 PLIP interactions: 27 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:K.166, D:E.194, D:H.287, D:S.368, D:S.368, D:G.369, D:G.370, D:G.393, D:G.394, C:N.111 Water bridges: D:K.168, D:K.168, D:H.291, D:H.291, D:H.291, D:H.291, D:H.291, D:S.368, D:S.368, D:M.371, D:G.395, C:E.48, C:E.48, C:N.54 Salt bridges: D:K.166, D:K.166, D:K.168, D:R.288, D:H.321, D:K.329, D:K.329 CAP.9: 26 residues within 4Å: Chain E: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, T.391, S.392, G.393, G.394 Chain F: E.48, T.53, N.54, N.111 Ligands: MG.10 26 PLIP interactions: 24 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:K.166, E:D.193, E:H.287, E:S.368, E:S.368, E:S.368, E:S.368, E:G.370, E:G.393, E:G.394, F:N.111 Water bridges: E:K.168, E:H.291, E:H.291, E:H.291, E:G.323, E:M.371, E:G.395, F:E.48 Salt bridges: E:K.166, E:K.166, E:K.168, E:R.288, E:H.321, E:K.329, E:K.329 CAP.11: 24 residues within 4Å: Chain E: E.48, T.53, N.111 Chain F: I.164, K.166, K.168, K.191, D.193, E.194, H.287, R.288, H.291, H.321, G.323, K.329, M.330, S.368, G.369, G.370, M.371, S.392, G.393, G.394 Ligands: MG.12 33 PLIP interactions: 29 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:K.166, F:E.194, F:H.287, F:S.368, F:S.368, F:S.368, F:G.370, F:T.391, F:G.393, F:G.394, E:T.53, E:T.53, E:N.111 Water bridges: F:K.168, F:R.288, F:R.288, F:H.291, F:H.291, F:G.323, F:G.323, F:K.329, F:M.371, F:M.371, F:M.371, F:G.395, E:E.48 Salt bridges: F:K.166, F:K.166, F:K.168, F:R.288, F:H.321, F:K.329, F:K.329

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: I.164, K.166, K.168, K.191, D.193, E.194, H.287 Chain B: N.111 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.193, A:E.194 MG.4: 9 residues within 4Å: Chain A: N.111 Chain B: I.164, K.166, K.168, K.191, D.193, E.194, H.287 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.193, B:E.194 MG.6: 9 residues within 4Å: Chain C: I.164, K.166, K.168, K.191, D.193, E.194, H.287 Chain D: N.111 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.193, C:E.194 MG.8: 9 residues within 4Å: Chain C: N.111 Chain D: I.164, K.166, K.168, K.191, D.193, E.194, H.287 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.193, D:E.194 MG.10: 7 residues within 4Å: Chain E: I.164, K.191, D.193, E.194, H.287 Chain F: N.111 Ligands: CAP.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.193, E:E.194, E:H.287 MG.12: 9 residues within 4Å: Chain E: N.111 Chain F: I.164, K.166, K.168, K.191, D.193, E.194, H.287 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.193, F:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, A.K. et al., Structural plasticity enables evolution and innovation of RuBisCO assemblies. Sci Adv (2022)

Release Date

2022-09-07

Peptides

Ribulose bisphosphate carboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
H

Ribulose bisphosphate carboxylase

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