SMTL ID : 4lf2.1 (3 other biounits)

Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-hexamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.187, K.212, D.214, E.215 Chain B: N.132 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.214, A:E.215, H2O.15 MG.5: 6 residues within 4Å: Chain A: N.132 Chain B: I.185, K.187, K.212, D.214, E.215 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain C: K.187, K.189, K.212, D.214, E.215 Chain D: N.132 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.214, C:E.215, H2O.38 MG.13: 6 residues within 4Å: Chain C: N.132 Chain D: K.187, K.189, K.212, D.214, E.215 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.214, D:E.215, H2O.29, H2O.38

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

SO4.2: 6 residues within 4Å: Chain A: R.309, H.312, H.342, M.351, S.389 Chain B: N.132 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:R.309, A:R.309, A:H.312, A:S.389, B:N.132 Salt bridges: A:R.309, A:H.342 Hydrogen bonds: B:N.132 SO4.3: 11 residues within 4Å: Chain A: I.185, K.187, K.350, G.390, G.391, T.412, A.413, G.414, G.415 Chain B: T.74, N.75 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.390, A:G.391, A:G.414, A:G.415, B:T.74, B:T.74 Water bridges: A:K.350, A:M.392, A:M.392, A:M.392, A:G.416 Salt bridges: A:K.187, A:K.350 SO4.6: 6 residues within 4Å: Chain B: R.309, H.312, H.342, G.344, M.351, S.389 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Water bridges: B:R.309, B:H.312, B:T.345, B:T.345, B:S.389, A:N.132 Salt bridges: B:R.309, B:H.342 SO4.7: 10 residues within 4Å: Chain A: T.74, N.75 Chain B: I.185, K.187, K.350, G.390, G.391, A.413, G.414, G.415 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.391, B:G.414, B:G.415, A:T.74, A:T.74 Water bridges: B:K.187, B:G.390 Salt bridges: B:K.187, B:K.350 SO4.10: 5 residues within 4Å: Chain C: R.309, H.312, H.342, M.351, S.389 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Water bridges: C:R.309, C:R.309, C:G.344, C:T.345, D:N.132 Salt bridges: C:R.309, C:H.342 SO4.11: 10 residues within 4Å: Chain C: I.185, K.187, K.350, G.390, G.391, A.413, G.414, G.415 Chain D: T.74, N.75 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:T.74, D:T.74, C:G.391, C:G.414, C:G.415 Salt bridges: C:K.187, C:K.350 SO4.14: 5 residues within 4Å: Chain D: R.309, H.312, H.342, M.351, S.389 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Water bridges: C:N.132, D:H.308, D:R.309, D:R.309, D:H.342, D:S.389 Salt bridges: D:R.309, D:H.342 SO4.15: 11 residues within 4Å: Chain C: T.74, N.75 Chain D: I.185, K.187, K.350, G.390, G.391, T.412, A.413, G.414, G.415 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.391, D:G.414, D:G.415, C:T.74, C:T.74 Water bridges: D:K.187, D:K.187, D:G.390, D:M.392, D:G.416, C:N.75 Salt bridges: D:K.187, D:K.350 SO4.16: 5 residues within 4Å: Chain E: R.309, H.312, H.342, M.351, S.389 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:H.342 Water bridges: E:H.312, E:H.312, E:G.344, E:T.345, E:T.345, E:E.352 Salt bridges: E:R.309, E:H.312 SO4.17: 11 residues within 4Å: Chain E: I.185, K.187, K.350, G.390, G.391, T.412, A.413, G.414, G.415 Chain F: T.74, N.75 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.390, E:G.391, E:G.414, E:G.415, F:T.74, F:T.74 Water bridges: E:K.350, E:M.392, E:G.416 Salt bridges: E:K.187, E:K.350 SO4.18: 4 residues within 4Å: Chain F: R.309, H.312, H.342, M.351 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:H.342 Water bridges: F:R.309, F:H.312, F:T.345, F:T.345, F:M.351, F:E.352 Salt bridges: F:R.309, F:H.312 SO4.19: 10 residues within 4Å: Chain E: T.74, N.75 Chain F: I.185, K.187, K.350, G.390, G.391, A.413, G.414, G.415 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.390, F:G.391, F:G.414, F:G.415, E:T.74, E:T.74 Water bridges: F:M.392, F:G.416 Salt bridges: F:K.187, F:K.350

3 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 4 residues within 4Å: Chain A: N.177, E.366, H.406, N.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.177, A:E.366, A:N.408 CO3.8: 3 residues within 4Å: Chain B: N.177, E.366, N.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.366 CO3.12: 2 residues within 4Å: Chain C: E.366, N.408 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.366

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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