SMTL ID : 5mac.1

Crystal structure of decameric Methanococcoides burtonii Rubisco complexed with 2-carboxyarabinitol bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-10-mer

Ligands

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

CAP.1: 21 residues within 4Å: Chain A: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Chain B: E.57, T.62, N.115 Ligands: MG.2 27 PLIP interactions: 23 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.167, A:E.196, A:G.401, A:G.424, A:S.425, B:T.62, B:N.115 Water bridges: A:K.169, A:K.169, A:H.288, A:R.289, A:H.322, A:S.399, A:S.399, A:L.402, A:L.402, A:L.402, A:G.426, B:E.57, B:E.57 Salt bridges: A:K.167, A:K.167, A:K.169, A:R.289, A:H.322, A:K.330, A:K.330 CAP.5: 23 residues within 4Å: Chain A: E.57, T.62, N.63, N.115 Chain B: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, T.422, M.423, G.424, S.425 Ligands: MG.6 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.167, B:S.399, B:G.401, B:T.422, B:G.424, B:S.425, A:T.62, A:T.62, A:N.115 Water bridges: B:K.169, B:H.288, B:R.289, B:R.289, B:H.322, B:K.330, B:S.399, B:S.399, B:L.402, B:L.402, B:L.402, B:G.426 Salt bridges: B:K.167, B:K.167, B:K.169, B:R.289, B:H.322, B:K.330, B:K.330 CAP.9: 22 residues within 4Å: Chain C: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, T.422, M.423, G.424, S.425 Chain D: E.57, T.62, N.115 Ligands: MG.10 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.167, C:E.196, C:E.196, C:S.399, C:S.399, C:G.400, C:G.401, C:G.424, C:S.425, D:T.62, D:N.115 Water bridges: C:R.289, C:H.292, C:G.324, C:K.330, C:S.399, C:L.402, C:L.402, C:G.426 Salt bridges: C:K.167, C:K.167, C:K.169, C:R.289, C:H.322, C:K.330, C:K.330 CAP.13: 21 residues within 4Å: Chain C: E.57, T.62, N.115 Chain D: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Ligands: MG.14 20 PLIP interactions: 3 interactions with chain C, 17 interactions with chain D Hydrogen bonds: C:T.62, C:T.62, C:N.115, D:K.167, D:D.195, D:S.399, D:G.401, D:G.424, D:S.425 Water bridges: D:K.330, D:S.399, D:L.402, D:T.422 Salt bridges: D:K.167, D:K.167, D:K.169, D:R.289, D:H.322, D:K.330, D:K.330 CAP.17: 21 residues within 4Å: Chain E: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Chain J: E.57, T.62, N.115 Ligands: MG.18 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:K.167, E:E.196, E:S.399, E:G.401, E:G.424, E:S.425, J:T.62, J:N.115 Salt bridges: E:K.167, E:K.167, E:K.169, E:R.289, E:H.322, E:K.330, E:K.330 CAP.21: 21 residues within 4Å: Chain F: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Chain G: E.57, T.62, N.115 Ligands: MG.22 26 PLIP interactions: 24 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:K.167, F:E.196, F:G.401, F:G.424, F:S.425, G:N.115 Water bridges: F:K.169, F:K.169, F:K.169, F:H.288, F:R.289, F:H.322, F:H.322, F:S.399, F:L.402, F:L.402, F:L.402, F:G.426, G:T.62 Salt bridges: F:K.167, F:K.167, F:K.169, F:R.289, F:H.322, F:K.330, F:K.330 CAP.25: 23 residues within 4Å: Chain F: E.57, T.62, N.63, N.115 Chain G: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, T.422, M.423, G.424, S.425 Ligands: MG.26 28 PLIP interactions: 25 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:K.167, G:S.399, G:G.401, G:T.422, G:G.424, G:S.425, F:T.62, F:T.62, F:N.115 Water bridges: G:K.169, G:H.288, G:R.289, G:R.289, G:H.322, G:K.330, G:S.399, G:S.399, G:L.402, G:L.402, G:L.402, G:G.426 Salt bridges: G:K.167, G:K.167, G:K.169, G:R.289, G:H.322, G:K.330, G:K.330 CAP.29: 22 residues within 4Å: Chain H: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, T.422, M.423, G.424, S.425 Chain I: E.57, T.62, N.115 Ligands: MG.30 26 PLIP interactions: 24 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:K.167, H:E.196, H:E.196, H:S.399, H:S.399, H:G.400, H:G.401, H:G.424, H:S.425, I:T.62, I:N.115 Water bridges: H:R.289, H:H.292, H:H.322, H:G.324, H:K.330, H:L.402, H:L.402, H:G.426 Salt bridges: H:K.167, H:K.167, H:K.169, H:R.289, H:H.322, H:K.330, H:K.330 CAP.33: 21 residues within 4Å: Chain H: E.57, T.62, N.115 Chain I: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Ligands: MG.34 20 PLIP interactions: 17 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:K.167, I:D.195, I:S.399, I:G.401, I:G.424, I:S.425, H:T.62, H:T.62, H:N.115 Water bridges: I:K.330, I:S.399, I:L.402, I:T.422 Salt bridges: I:K.167, I:K.167, I:K.169, I:R.289, I:H.322, I:K.330, I:K.330 CAP.37: 21 residues within 4Å: Chain E: E.57, T.62, N.115 Chain J: I.165, K.167, K.169, K.193, D.195, E.196, H.288, R.289, H.322, K.330, M.331, S.399, G.400, G.401, M.423, G.424, S.425 Ligands: MG.38 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:K.167, J:E.196, J:S.399, J:G.401, J:G.424, J:S.425, E:N.115 Salt bridges: J:K.167, J:K.167, J:K.169, J:R.289, J:H.322, J:K.330, J:K.330

20 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.167, K.193, D.195, E.196 Chain B: N.115 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.195, A:E.196 MG.3: 4 residues within 4Å: Chain A: D.366, D.368 Chain G: E.179, D.183 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain A Metal complexes: G:E.179, G:D.183, G:D.183, A:D.366, A:D.368 MG.6: 7 residues within 4Å: Chain A: N.115 Chain B: K.167, K.169, K.193, D.195, E.196 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.195, B:E.196 MG.7: 4 residues within 4Å: Chain B: D.366, D.368 Chain D: E.179, D.183 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.179, D:D.183, B:D.366, B:D.368, H2O.7 MG.10: 5 residues within 4Å: Chain C: K.193, D.195, E.196 Chain D: N.115 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.195, C:E.196 MG.11: 4 residues within 4Å: Chain A: E.179, D.183 Chain C: D.366, D.368 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.366, C:D.366, A:D.183, A:D.183, H2O.9 MG.14: 6 residues within 4Å: Chain C: N.115 Chain D: K.169, K.193, D.195, E.196 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.195, D:E.196 MG.15: 4 residues within 4Å: Chain D: D.366, D.368 Chain J: E.179, D.183 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain J Metal complexes: D:D.366, D:D.366, D:D.368, J:E.179, J:D.183 MG.18: 4 residues within 4Å: Chain E: K.193, D.195, E.196 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.195, E:E.196 MG.19: 4 residues within 4Å: Chain C: E.179, D.183 Chain E: D.366, D.368 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:D.366, C:E.179, C:D.183, C:D.183, H2O.11 MG.22: 6 residues within 4Å: Chain F: K.167, K.193, D.195, E.196 Chain G: N.115 Ligands: CAP.21 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.195, F:E.196 MG.23: 4 residues within 4Å: Chain B: E.179, D.183 Chain F: D.366, D.368 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain B Metal complexes: F:D.366, F:D.368, B:E.179, B:D.183, B:D.183 MG.26: 7 residues within 4Å: Chain F: N.115 Chain G: K.167, K.169, K.193, D.195, E.196 Ligands: CAP.25 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.195, G:E.196 MG.27: 4 residues within 4Å: Chain G: D.366, D.368 Chain I: E.179, D.183 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: I:E.179, I:D.183, G:D.366, G:D.368, H2O.18 MG.30: 5 residues within 4Å: Chain H: K.193, D.195, E.196 Chain I: N.115 Ligands: CAP.29 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.195, H:E.196 MG.31: 4 residues within 4Å: Chain F: E.179, D.183 Chain H: D.366, D.368 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: F:D.183, F:D.183, H:D.366, H:D.366, H2O.20 MG.34: 6 residues within 4Å: Chain H: N.115 Chain I: K.169, K.193, D.195, E.196 Ligands: CAP.33 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.195, I:E.196 MG.35: 4 residues within 4Å: Chain E: E.179, D.183 Chain I: D.366, D.368 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain E Metal complexes: I:D.366, I:D.366, I:D.368, E:E.179, E:D.183 MG.38: 4 residues within 4Å: Chain J: K.193, D.195, E.196 Ligands: CAP.37 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.195, J:E.196 MG.39: 4 residues within 4Å: Chain H: E.179, D.183 Chain J: D.366, D.368 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: H:E.179, H:D.183, H:D.183, J:D.366, H2O.22

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: L.22 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: D.21, L.22 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: L.22 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain D: L.22 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain E: L.22 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain F: L.22 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain G: D.21, L.22 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain H: L.22 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain I: L.22 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain J: L.22 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunn, L.H. et al., A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic. J. Biol. Chem. (2017)

Release Date

2017-02-08

Peptides

Ribulose-1,5-bisphosphate carboxylase-oxygenase type III: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Ribulose-1,5-bisphosphate carboxylase-oxygenase type III