SMTL ID : 5hqm.1

Structure function studies of R. palustris RubisCO (R. palustris/R. rubrum chimera)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

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

CAP.1: 25 residues within 4Å: Chain A: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Chain B: E.69, T.74, N.132 Ligands: MG.2 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.187, A:H.308, A:H.312, A:S.389, A:S.389, A:G.391, A:G.414, A:G.415, B:T.74, B:T.74, B:N.132 Water bridges: A:K.189, A:K.189, A:K.189, A:R.309, A:R.309, A:H.342, A:S.389, A:M.392, A:M.392, A:M.392, A:G.416 Salt bridges: A:K.187, A:K.187, A:K.189, A:R.309, A:H.342, A:K.350, A:K.350 CAP.4: 25 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.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Ligands: MG.5 26 PLIP interactions: 22 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.187, B:D.214, B:H.308, B:S.389, B:S.389, B:G.391, B:G.414, B:G.415, A:T.74, A:T.74, A:N.132 Water bridges: B:K.189, B:K.189, B:H.312, B:G.390, B:M.392, B:M.392, B:G.416, A:E.69 Salt bridges: B:K.187, B:K.187, B:K.189, B:R.309, B:H.342, B:K.350, B:K.350 CAP.7: 25 residues within 4Å: Chain C: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Chain D: E.69, T.74, N.132 Ligands: MG.8 29 PLIP interactions: 26 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.187, C:H.308, C:H.312, C:S.389, C:S.389, C:G.391, C:G.414, C:G.415, D:T.74, D:T.74, D:N.132 Water bridges: C:K.189, C:K.189, C:K.189, C:R.309, C:R.309, C:H.342, C:S.389, C:M.392, C:M.392, C:M.392, C:G.416 Salt bridges: C:K.187, C:K.187, C:K.189, C:R.309, C:H.342, C:K.350, C:K.350 CAP.10: 25 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.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Ligands: MG.11 26 PLIP interactions: 22 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:K.187, D:D.214, D:H.308, D:S.389, 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:K.189, D:H.312, D:G.390, D:M.392, D:M.392, D:G.416, C:E.69 Salt bridges: D:K.187, D:K.187, D:K.189, D:R.309, D:H.342, D:K.350, D:K.350 CAP.13: 25 residues within 4Å: Chain E: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Chain F: E.69, T.74, N.132 Ligands: MG.14 29 PLIP interactions: 3 interactions with chain F, 26 interactions with chain E Hydrogen bonds: F:T.74, F:T.74, F:N.132, E:K.187, E:H.308, E:H.312, E:S.389, E:S.389, E:G.391, E:G.414, E:G.415 Water bridges: E:K.189, E:K.189, E:K.189, E:R.309, E:R.309, E:H.342, E:S.389, E:M.392, 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.16: 25 residues within 4Å: Chain E: E.69, T.74, N.132 Chain F: I.185, K.187, K.189, K.212, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Ligands: MG.17 26 PLIP interactions: 22 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:K.187, F:D.214, F:H.308, F:S.389, F:S.389, F:G.391, F:G.414, F:G.415, E:T.74, E:T.74, E:N.132 Water bridges: F:K.189, F:K.189, F:H.312, F:G.390, F:M.392, F:M.392, F:G.416, E:E.69 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: 9 residues within 4Å: Chain A: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Chain B: N.132 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.214, A:E.215 MG.5: 9 residues within 4Å: Chain A: N.132 Chain B: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.214, B:E.215 MG.8: 9 residues within 4Å: Chain C: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Chain D: N.132 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.214, C:E.215 MG.11: 9 residues within 4Å: Chain C: N.132 Chain D: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.214, D:E.215 MG.14: 9 residues within 4Å: Chain E: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Chain F: N.132 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.214, E:E.215 MG.17: 9 residues within 4Å: Chain E: N.132 Chain F: I.185, K.187, K.189, K.212, D.214, E.215, H.308 Ligands: CAP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.214, F:E.215

6 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: L.30, L.32, K.33, Y.93, E.94 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.30, A:L.32, A:Y.93 K.6: 5 residues within 4Å: Chain B: L.30, L.32, K.33, Y.93, E.94 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.30, B:L.32, B:Y.93, H2O.13 K.9: 5 residues within 4Å: Chain C: L.30, L.32, K.33, Y.93, E.94 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:L.30, C:L.32, C:Y.93 K.12: 5 residues within 4Å: Chain D: L.30, L.32, K.33, Y.93, E.94 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.30, D:L.32, D:Y.93, H2O.29 K.15: 5 residues within 4Å: Chain E: L.30, L.32, K.33, Y.93, E.94 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:L.30, E:L.32, E:Y.93 K.18: 5 residues within 4Å: Chain F: L.30, L.32, K.33, Y.93, E.94 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:L.30, F:L.32, F:Y.93, H2O.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arbing, M.A. et al., Structure function studies of R. palustris RubisCO. To Be Published

Release Date

2017-01-25

Peptides

Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Ribulose bisphosphate carboxylase (R. palustris/R. rubrum chimera),Ribulose bisphosphate carboxylase