SMTL ID : 7qsz.1

Non-obligately L8S8-complex forming RubisCO derived from ancestral sequence reconstruction and rational engineering in L8 complex with substitution e170N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

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

CAP.1: 22 residues within 4Å: Chain A: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Chain H: E.53, T.58, W.59, N.109 Ligands: MG.2 31 PLIP interactions: 27 interactions with chain A, 4 interactions with chain H Hydrogen bonds: A:T.159, A:T.159, A:K.161, A:E.190, A:H.284, A:S.365, A:G.367, A:G.389, A:G.390, H:T.58, H:T.58, H:N.109 Water bridges: A:T.159, A:K.163, A:K.163, A:K.163, A:R.281, A:G.315, A:S.365, A:G.366, A:I.368, A:I.368, A:G.391, H:E.53 Salt bridges: A:K.161, A:K.161, A:K.163, A:R.281, A:H.313, A:K.320, A:K.320 CAP.3: 22 residues within 4Å: Chain B: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Chain G: E.53, T.58, W.59, N.109 Ligands: MG.4 32 PLIP interactions: 29 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:T.159, B:T.159, B:K.161, B:E.190, B:H.284, B:S.365, B:G.367, B:G.389, B:G.390, G:T.58, G:T.58, G:N.109 Water bridges: B:T.159, B:K.163, B:K.163, B:K.163, B:R.281, B:R.281, B:G.315, B:G.315, B:K.320, B:I.368, B:I.368, B:L.387, B:G.391 Salt bridges: B:K.161, B:K.161, B:K.163, B:R.281, B:H.313, B:K.320, B:K.320 CAP.5: 21 residues within 4Å: Chain C: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Chain F: E.53, T.58, W.59, N.109 Ligands: MG.6 29 PLIP interactions: 27 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:T.159, C:T.159, C:K.161, C:G.367, C:G.389, C:G.390, F:T.58, F:N.109 Water bridges: C:T.159, C:K.163, C:K.163, C:K.163, C:K.163, C:H.280, C:R.281, C:R.281, C:H.313, C:G.315, C:S.365, C:G.366, C:I.368, C:G.391 Salt bridges: C:K.161, C:K.161, C:K.163, C:R.281, C:H.313, C:K.320, C:K.320 CAP.7: 22 residues within 4Å: Chain D: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Chain E: E.53, T.58, W.59, N.109 Ligands: MG.8 33 PLIP interactions: 30 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:T.159, D:T.159, D:K.161, D:G.367, D:G.389, D:G.390, E:T.58, E:T.58, E:N.109 Water bridges: D:T.159, D:T.159, D:K.163, D:K.163, D:K.163, D:H.280, D:R.281, D:R.281, D:R.281, D:H.313, D:G.315, D:K.320, D:S.365, D:G.366, D:I.368, D:I.368, D:G.391 Salt bridges: D:K.161, D:K.161, D:K.163, D:R.281, D:H.313, D:K.320, D:K.320 CAP.9: 22 residues within 4Å: Chain D: E.53, T.58, W.59, N.109 Chain E: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Ligands: MG.10 31 PLIP interactions: 28 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:T.159, E:K.161, E:E.190, E:H.284, E:S.365, E:G.367, E:G.389, E:G.390, D:T.58, D:T.58, D:N.109 Water bridges: E:T.159, E:T.159, E:K.163, E:K.163, E:K.163, E:K.163, E:R.281, E:G.315, E:S.365, E:G.366, E:I.368, E:I.368, E:G.391 Salt bridges: E:K.161, E:K.161, E:K.163, E:R.281, E:H.313, E:K.320, E:K.320 CAP.11: 22 residues within 4Å: Chain C: E.53, T.58, W.59, N.109 Chain F: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Ligands: MG.12 33 PLIP interactions: 29 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:T.159, F:K.161, F:E.190, F:E.190, F:H.284, F:S.365, F:G.367, F:G.389, F:G.390, C:T.58, C:T.58, C:N.109 Water bridges: F:T.159, F:T.159, F:K.163, F:K.163, F:R.281, F:R.281, F:G.315, F:G.315, F:K.320, F:I.368, F:I.368, F:L.387, F:G.391, C:E.53 Salt bridges: F:K.161, F:K.161, F:K.163, F:R.281, F:H.313, F:K.320, F:K.320 CAP.13: 21 residues within 4Å: Chain B: E.53, T.58, W.59, N.109 Chain G: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Ligands: MG.14 29 PLIP interactions: 27 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:T.159, G:K.161, G:G.367, G:G.389, G:G.390, B:T.58, B:N.109 Water bridges: G:T.159, G:T.159, G:K.163, G:K.163, G:K.163, G:K.163, G:H.280, G:R.281, G:R.281, G:H.313, G:G.315, G:S.365, G:G.366, G:I.368, G:G.391 Salt bridges: G:K.161, G:K.161, G:K.163, G:R.281, G:H.313, G:K.320, G:K.320 CAP.15: 22 residues within 4Å: Chain A: E.53, T.58, W.59, N.109 Chain H: T.159, K.161, K.163, K.187, D.189, E.190, H.280, R.281, H.284, H.313, K.320, L.321, S.365, G.366, G.367, G.389, G.390 Ligands: MG.16 32 PLIP interactions: 28 interactions with chain H, 4 interactions with chain A Hydrogen bonds: H:T.159, H:K.161, H:G.367, H:G.389, H:G.390, A:T.58, A:T.58, A:N.109 Water bridges: H:T.159, H:T.159, H:K.163, H:K.163, H:H.280, H:R.281, H:R.281, H:R.281, H:H.313, H:G.315, H:K.320, H:S.365, H:G.366, H:I.368, H:I.368, H:G.391, A:E.53 Salt bridges: H:K.161, H:K.161, H:K.163, H:R.281, H:H.313, H:K.320, H:K.320

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: T.159, K.161, K.163, K.187, D.189, E.190 Chain H: N.109 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.189, A:E.190 MG.4: 7 residues within 4Å: Chain B: T.159, K.163, K.187, D.189, E.190 Chain G: N.109 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.189, B:E.190 MG.6: 7 residues within 4Å: Chain C: T.159, K.161, K.163, K.187, D.189, E.190 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.189, C:E.190 MG.8: 6 residues within 4Å: Chain D: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.189, D:E.190 MG.10: 8 residues within 4Å: Chain D: N.109 Chain E: T.159, K.161, K.163, K.187, D.189, E.190 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.189, E:E.190 MG.12: 7 residues within 4Å: Chain C: N.109 Chain F: T.159, K.163, K.187, D.189, E.190 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.189, F:E.190 MG.14: 7 residues within 4Å: Chain G: T.159, K.161, K.163, K.187, D.189, E.190 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.189, G:E.190 MG.16: 6 residues within 4Å: Chain H: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.189, H:E.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, L. et al., Evolution of increased complexity and specificity at the dawn of form I Rubiscos. Science (2022)

Release Date

2022-10-12

Peptides

RubisCO large subunit: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

RubisCO large subunit

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