SMTL ID : 6ura.1

Crystal structure of RUBISCO from Promineofilum breve

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-octamer

Ligands

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

CAP.1: 24 residues within 4Å: Chain A: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Chain B: E.71, T.76, W.77, N.127 Ligands: MG.2 37 PLIP interactions: 32 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.177, A:K.179, A:E.208, A:H.298, A:S.383, A:S.383, A:G.385, A:G.407, A:G.408, B:T.76, B:T.76, B:W.77, B:N.127 Water bridges: A:T.177, A:T.177, A:K.181, A:K.181, A:R.299, A:R.299, A:H.302, A:H.302, A:H.331, A:G.333, A:K.338, A:S.383, A:G.384, A:G.384, A:I.386, A:I.386, B:E.71 Salt bridges: A:K.179, A:K.179, A:K.181, A:R.299, A:H.331, A:K.338, A:K.338 CAP.3: 24 residues within 4Å: Chain A: E.71, T.76, W.77, N.127 Chain B: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Ligands: MG.4 34 PLIP interactions: 30 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.179, B:H.298, B:S.383, B:G.385, B:G.407, B:G.408, A:T.76, A:T.76, A:W.77, A:N.127 Water bridges: B:T.177, B:K.181, B:K.181, B:R.299, B:R.299, B:R.299, B:R.299, B:H.302, B:H.302, B:H.331, B:G.333, B:K.338, B:K.338, B:G.384, B:I.386, B:I.386, B:G.409 Salt bridges: B:K.179, B:K.179, B:K.181, B:R.299, B:H.331, B:K.338, B:K.338 CAP.5: 24 residues within 4Å: Chain C: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Chain D: E.71, T.76, W.77, N.127 Ligands: MG.6 37 PLIP interactions: 33 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.177, C:K.179, C:E.208, C:H.298, C:S.383, C:S.383, C:G.385, C:G.407, C:G.408, D:T.76, D:T.76, D:W.77, D:N.127 Water bridges: C:T.177, C:T.177, C:K.181, C:K.181, C:K.181, C:R.299, C:R.299, C:H.302, C:H.302, C:H.331, C:G.333, C:K.338, C:S.383, C:G.384, C:G.384, C:I.386, C:I.386 Salt bridges: C:K.179, C:K.179, C:K.181, C:R.299, C:H.331, C:K.338, C:K.338 CAP.7: 24 residues within 4Å: Chain C: E.71, T.76, W.77, N.127 Chain D: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Ligands: MG.8 34 PLIP interactions: 29 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:K.179, D:H.298, D:S.383, D:G.385, D:G.407, D:G.408, C:T.76, C:T.76, C:W.77, C:N.127 Water bridges: D:T.177, D:K.181, D:R.299, D:R.299, D:R.299, D:R.299, D:H.302, D:H.302, D:H.331, D:G.333, D:K.338, D:K.338, D:G.384, D:I.386, D:I.386, D:G.409, C:E.71 Salt bridges: D:K.179, D:K.179, D:K.181, D:R.299, D:H.331, D:K.338, D:K.338 CAP.9: 24 residues within 4Å: Chain E: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Chain F: E.71, T.76, W.77, N.127 Ligands: MG.10 33 PLIP interactions: 29 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:T.177, E:K.179, E:H.298, E:S.383, E:S.383, E:G.385, E:G.407, E:G.408, F:T.76, F:W.77, F:N.127 Water bridges: E:T.177, E:T.177, E:K.181, E:K.181, E:H.302, E:H.302, E:H.302, E:G.333, E:K.338, E:S.383, E:G.384, E:I.386, E:I.386, E:I.386, F:E.71 Salt bridges: E:K.179, E:K.179, E:K.181, E:R.299, E:H.331, E:K.338, E:K.338 CAP.11: 23 residues within 4Å: Chain E: E.71, T.76, W.77, N.127 Chain F: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Ligands: MG.12 32 PLIP interactions: 28 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:T.177, F:K.179, F:H.298, F:G.384, F:G.385, F:G.407, F:G.408, E:T.76, E:T.76, E:W.77, E:N.127 Water bridges: F:T.177, F:T.177, F:K.181, F:K.181, F:H.302, F:H.331, F:K.338, F:K.338, F:S.383, F:S.383, F:S.383, F:I.386, F:I.386, F:G.409 Salt bridges: F:K.179, F:K.179, F:K.181, F:R.299, F:H.331, F:K.338, F:K.338 CAP.13: 24 residues within 4Å: Chain G: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.302, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Chain H: E.71, T.76, W.77, N.127 Ligands: MG.14 33 PLIP interactions: 3 interactions with chain H, 30 interactions with chain G Hydrogen bonds: H:T.76, H:W.77, H:N.127, G:T.177, G:K.179, G:H.298, G:S.383, G:S.383, G:G.385, G:G.407, G:G.408 Water bridges: G:T.177, G:T.177, G:K.181, G:K.181, G:K.181, G:H.302, G:H.302, G:H.302, G:G.333, G:K.338, G:S.383, G:G.384, G:I.386, G:I.386, G:I.386 Salt bridges: G:K.179, G:K.179, G:K.181, G:R.299, G:H.331, G:K.338, G:K.338 CAP.15: 23 residues within 4Å: Chain G: E.71, T.76, W.77, N.127 Chain H: T.177, K.179, K.181, K.205, D.207, E.208, H.298, R.299, H.331, G.333, K.338, L.339, S.383, G.384, G.385, F.406, G.407, G.408 Ligands: MG.16 32 PLIP interactions: 27 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:T.177, H:K.179, H:H.298, H:G.384, H:G.385, H:G.407, H:G.408, G:T.76, G:T.76, G:W.77, G:N.127 Water bridges: H:T.177, H:T.177, H:K.181, H:H.302, H:H.331, H:K.338, H:K.338, H:S.383, H:S.383, H:S.383, H:I.386, H:I.386, H:G.409, G:E.71 Salt bridges: H:K.179, H:K.179, H:K.181, H:R.299, H:H.331, H:K.338, H:K.338

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Chain B: N.127 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.207, A:E.208 MG.4: 9 residues within 4Å: Chain A: N.127 Chain B: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.207, B:E.208 MG.6: 9 residues within 4Å: Chain C: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Chain D: N.127 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.207, C:E.208 MG.8: 9 residues within 4Å: Chain C: N.127 Chain D: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.207, D:E.208 MG.10: 9 residues within 4Å: Chain E: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Chain F: N.127 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.207, E:E.208 MG.12: 9 residues within 4Å: Chain E: N.127 Chain F: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.207, F:E.208 MG.14: 9 residues within 4Å: Chain G: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Chain H: N.127 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.207, G:E.208 MG.16: 9 residues within 4Å: Chain G: N.127 Chain H: T.177, K.179, K.181, K.205, D.207, E.208, H.298 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.207, H:E.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banda, D.M. et al., Novel bacterial clade reveals origin of form I Rubisco. Nat.Plants (2020)

Release Date

2020-08-19

Peptides

Ribulose bisphosphate carboxylase large chain: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
C

F
D

G
C

H
D

Ribulose bisphosphate carboxylase large chain