SMTL ID : 4lf1.1 (3 other biounits)

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with 2-CABP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-hexamer

Ligands

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

CAP.1: 20 residues within 4Å: Chain A: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, S.389, G.390, G.391, A.413, G.414, G.415 Chain B: E.69, T.74, N.132 Ligands: MG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.187, A:S.389, A:G.391, A:G.414, A:G.415, B:T.74, B:T.74, B:N.132 Water bridges: A:R.309, A:H.312, A:G.344, A:G.390 Salt bridges: A:K.187, A:K.187, A:K.189, A:R.309, A:H.342, A:K.350, A:K.350 CAP.3: 21 residues within 4Å: Chain A: E.69, T.74, N.132 Chain B: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, M.351, S.389, G.390, G.391, A.413, G.414, G.415 Ligands: MG.4 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.187, B:S.389, B:G.391, B:G.414, B:G.415, A:T.74, A:T.74, A:N.132 Water bridges: B:R.309, B:R.309, B:H.312, B:G.344, B:M.392, B:M.392, B:M.392 Salt bridges: B:K.187, B:K.187, B:K.189, B:R.309, B:H.342, B:K.350, B:K.350 CAP.5: 21 residues within 4Å: Chain C: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, M.351, S.389, G.390, G.391, A.413, G.414, G.415 Chain D: E.69, T.74, N.132 Ligands: MG.6 23 PLIP interactions: 20 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.187, C:E.215, C:S.389, C:G.391, C:G.414, C:G.415, D:T.74, D:N.132 Water bridges: C:R.309, C:R.309, C:K.350, C:S.389, C:G.390, C:M.392, C:M.392, D:T.74 Salt bridges: C:K.187, C:K.187, C:K.189, C:R.309, C:H.342, C:K.350, C:K.350 CAP.7: 20 residues within 4Å: Chain C: E.69, T.74, N.132 Chain D: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, S.389, G.390, G.391, A.413, G.414, G.415 Ligands: MG.8 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:K.187, D:S.389, D:G.391, D:G.414, D:G.415, C:T.74, C:T.74, C:N.132 Water bridges: D:K.189, D:R.309, D:R.309, D:A.310, D:H.312, D:G.344, D:G.390, D:G.416, D:G.416, C:N.132 Salt bridges: D:K.187, D:K.187, D:K.189, D:R.309, D:H.342, D:K.350, D:K.350 CAP.9: 21 residues within 4Å: Chain E: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, M.351, S.389, G.390, G.391, A.413, G.414, G.415 Chain F: E.69, T.74, N.132 Ligands: MG.10 23 PLIP interactions: 20 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:K.187, E:S.389, E:G.391, E:G.414, E:G.415, F:T.74, F:T.74, F:N.132 Water bridges: E:R.309, E:R.309, E:R.309, E:H.312, E:G.344, E:M.392, E:M.392, E:G.416 Salt bridges: E:K.187, E:K.187, E:K.189, E:R.309, E:H.342, E:K.350, E:K.350 CAP.11: 22 residues within 4Å: Chain E: E.69, T.74, N.75, N.132 Chain F: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.342, K.350, M.351, S.389, G.390, G.391, A.413, G.414, G.415 Ligands: MG.12 24 PLIP interactions: 20 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:K.187, F:S.389, F:G.391, F:G.414, F:G.415, E:T.74, E:T.74, E:N.75, E:N.132 Water bridges: F:R.309, F:R.309, F:H.312, F:K.350, F:K.350, F:S.389, F:S.389, F:G.390 Salt bridges: F:K.187, F:K.187, F:K.189, F:R.309, F:H.342, F:K.350, F:K.350

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.187, K.189, K.212, D.214, E.215 Chain B: N.132 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.214, A:E.215 MG.4: 6 residues within 4Å: Chain A: N.132 Chain B: K.212, D.214, E.215, H.308 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.214, B:E.215 MG.6: 8 residues within 4Å: Chain C: I.185, K.187, K.189, K.212, D.214, E.215 Chain D: N.132 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.214, C:E.215 MG.8: 7 residues within 4Å: Chain C: N.132 Chain D: K.187, K.189, K.212, D.214, E.215 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.214, D:E.215 MG.10: 7 residues within 4Å: Chain E: K.187, K.189, K.212, D.214, E.215 Chain F: N.132 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.214, E:E.215 MG.12: 5 residues within 4Å: Chain F: K.187, K.212, D.214, E.215 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.214, F:E.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satagopan, S. et al., Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris. J.Biol.Chem. (2014)

Release Date

2014-06-25

Peptides

Ribulose bisphosphate carboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ribulose bisphosphate carboxylase

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