SMTL ID : 5hk4.1

Structure function studies of R. palustris RubisCO (A47V-M331A mutant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

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

CAP.1: 23 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, S.389, G.390, G.391, M.392, A.413, G.414, G.415 Chain B: E.69, T.74, N.132 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.187, A:H.308, A:S.389, A:S.389, A:G.391, A:G.414, A:G.415, B:T.74, B:N.132 Water bridges: A:R.309, A:A.310, A:H.312, A:G.344 Salt bridges: A:K.187, A:K.187, A:K.189, A:R.309, A:H.312, A:H.342, A:K.350, A:K.350 CAP.3: 24 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, S.389, G.390, G.391, M.392, A.413, G.414, G.415, G.416 Ligands: MG.4 27 PLIP interactions: 24 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.187, B:H.308, B:H.312, 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:R.309, B:R.309, B:G.344, B:M.392, B:M.392, B:M.392, B:G.416 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: 23 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, S.389, G.390, G.391, M.392, A.413, G.414, G.415 Chain D: E.69, T.74, N.132 Ligands: MG.6 27 PLIP interactions: 24 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:R.309, C:R.309, C:A.310, C:H.342, C:T.345, C:S.389, C:G.390, C:M.392 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: 24 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, S.389, G.390, G.391, M.392, T.412, A.413, G.414, G.415 Ligands: MG.8 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.187, D:E.215, D:H.308, D:H.312, D:S.389, D:S.389, D:S.389, D:G.391, D:G.414, D:G.415, C:T.74, C:N.132 Water bridges: D:K.189, D:R.309, D:H.342, D:G.344, D:G.390, D:M.392, D:M.392, D:G.416 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: 22 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, S.389, G.390, G.391, A.413, G.414, G.415 Chain F: E.69, T.74, N.132 Ligands: MG.10 30 PLIP interactions: 27 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:K.187, E:E.215, E:H.308, E:H.312, E:S.389, E:S.389, E:G.391, E:T.412, E:G.414, E:G.415, F:T.74, F:T.74, F:N.132 Water bridges: E:K.189, E:K.189, E:K.189, E:K.189, E:R.309, E:G.344, E:G.390, 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: 24 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, S.389, G.390, G.391, M.392, T.412, A.413, G.414, G.415 Ligands: MG.12 31 PLIP interactions: 27 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:K.187, F:D.214, F:H.308, F:H.312, F:S.389, F:S.389, F:S.389, F:G.391, F:T.412, F:G.414, F:G.415, E:T.74, E:T.74, E:N.132 Water bridges: F:K.189, F:R.309, F:R.309, F:R.309, F:A.310, F:S.389, 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.4: 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.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.214, B:E.215 MG.6: 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.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.214, C:E.215 MG.8: 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.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.214, D:E.215 MG.10: 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.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.214, E:E.215 MG.12: 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.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

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

Release Date

2017-01-18

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