SMTL ID : 7qsw.1

L8S8-complex forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of SSU-bearing Form I RubisCOs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-8-8-mer

Ligands

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

CAP.1: 22 residues within 4Å: Chain A: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, F.400, G.401, G.402 Chain O: E.58, T.63, W.64, N.121 Ligands: MG.2 32 PLIP interactions: 28 interactions with chain A, 4 interactions with chain O Hydrogen bonds: A:T.171, A:T.171, A:K.173, A:E.202, A:H.296, A:S.377, A:G.379, A:G.401, A:G.402, O:T.63, O:T.63, O:N.121 Water bridges: A:T.171, A:T.171, A:K.175, A:K.175, A:K.175, A:R.293, A:R.293, A:G.327, A:G.327, A:G.378, A:I.380, A:G.403, O:E.58 Salt bridges: A:K.173, A:K.173, A:K.175, A:R.293, A:H.325, A:K.332, A:K.332 CAP.3: 21 residues within 4Å: Chain C: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Chain K: E.58, T.63, W.64, N.121 Ligands: MG.4 29 PLIP interactions: 26 interactions with chain C, 3 interactions with chain K Hydrogen bonds: C:T.171, C:T.171, C:K.173, C:H.296, C:S.377, C:G.379, C:G.401, C:G.402, K:T.63, K:N.121 Water bridges: C:T.171, C:T.171, C:K.175, C:K.175, C:K.175, C:R.293, C:R.293, C:G.327, C:G.378, C:I.380, C:G.403, K:T.63 Salt bridges: C:K.173, C:K.173, C:K.175, C:R.293, C:H.325, C:K.332, C:K.332 CAP.5: 21 residues within 4Å: Chain E: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Chain M: E.58, T.63, W.64, N.121 Ligands: MG.6 30 PLIP interactions: 28 interactions with chain E, 2 interactions with chain M Hydrogen bonds: E:T.171, E:K.173, E:E.202, E:G.379, E:G.401, E:G.402, M:T.63, M:N.121 Water bridges: E:T.171, E:K.175, E:K.175, E:K.175, E:K.175, E:H.292, E:R.293, E:R.293, E:H.325, E:G.327, E:G.327, E:S.377, E:G.378, E:I.380, E:G.403 Salt bridges: E:K.173, E:K.173, E:K.175, E:R.293, E:H.325, E:K.332, E:K.332 CAP.7: 21 residues within 4Å: Chain G: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Chain I: E.58, T.63, W.64, N.121 Ligands: MG.8 28 PLIP interactions: 26 interactions with chain G, 2 interactions with chain I Hydrogen bonds: G:T.171, G:K.173, G:G.379, G:G.401, G:G.402, I:T.63, I:N.121 Water bridges: G:T.171, G:K.175, G:K.175, G:K.175, G:K.175, G:H.292, G:R.293, G:R.293, G:G.327, G:G.327, G:S.377, G:G.378, G:I.380, G:G.403 Salt bridges: G:K.173, G:K.173, G:K.175, G:R.293, G:H.325, G:K.332, G:K.332 CAP.9: 22 residues within 4Å: Chain G: E.58, T.63, W.64, N.121 Chain I: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, F.400, G.401, G.402 Ligands: MG.10 31 PLIP interactions: 28 interactions with chain I, 3 interactions with chain G Hydrogen bonds: I:T.171, I:K.173, I:E.202, I:H.296, I:S.377, I:G.379, I:G.401, I:G.402, G:T.63, G:T.63, G:N.121 Water bridges: I:T.171, I:T.171, I:K.175, I:K.175, I:K.175, I:K.175, I:R.293, I:R.293, I:G.327, I:G.327, I:G.378, I:I.380, I:G.403 Salt bridges: I:K.173, I:K.173, I:K.175, I:R.293, I:H.325, I:K.332, I:K.332 CAP.11: 21 residues within 4Å: Chain C: E.58, T.63, W.64, N.121 Chain K: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Ligands: MG.12 29 PLIP interactions: 26 interactions with chain K, 3 interactions with chain C Hydrogen bonds: K:T.171, K:K.173, K:H.296, K:S.377, K:G.379, K:G.401, K:G.402, C:T.63, C:T.63, C:N.121 Water bridges: K:T.171, K:T.171, K:K.175, K:K.175, K:K.175, K:K.175, K:R.293, K:R.293, K:G.327, K:G.378, K:I.380, K:G.403 Salt bridges: K:K.173, K:K.173, K:K.175, K:R.293, K:H.325, K:K.332, K:K.332 CAP.13: 21 residues within 4Å: Chain E: E.58, T.63, W.64, N.121 Chain M: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Ligands: MG.14 30 PLIP interactions: 27 interactions with chain M, 3 interactions with chain E Hydrogen bonds: M:T.171, M:T.171, M:K.173, M:E.202, M:G.379, M:G.401, M:G.402, E:N.121 Water bridges: M:T.171, M:K.175, M:K.175, M:R.293, M:R.293, M:H.325, M:H.325, M:G.327, M:G.327, M:S.377, M:G.378, M:I.380, M:G.403, E:E.58, E:T.63 Salt bridges: M:K.173, M:K.173, M:K.175, M:R.293, M:H.325, M:K.332, M:K.332 CAP.15: 21 residues within 4Å: Chain A: E.58, T.63, W.64, N.121 Chain O: T.171, K.173, K.175, K.199, D.201, E.202, H.292, R.293, H.325, K.332, L.333, S.377, G.378, G.379, G.401, G.402 Ligands: MG.16 29 PLIP interactions: 27 interactions with chain O, 2 interactions with chain A Hydrogen bonds: O:T.171, O:T.171, O:K.173, O:G.379, O:G.401, O:G.402, A:N.121 Water bridges: O:T.171, O:K.175, O:K.175, O:K.175, O:H.292, O:R.293, O:R.293, O:H.325, O:G.327, O:G.327, O:S.377, O:G.378, O:I.380, O:G.403, A:T.63 Salt bridges: O:K.173, O:K.173, O:K.175, O:R.293, O:H.325, O:K.332, O:K.332

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Chain O: N.121 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.201, A:E.202 MG.4: 9 residues within 4Å: Chain C: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Chain K: N.121 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.201, C:E.202 MG.6: 9 residues within 4Å: Chain E: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Chain M: N.121 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.201, E:E.202 MG.8: 9 residues within 4Å: Chain G: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Chain I: N.121 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.201, G:E.202 MG.10: 9 residues within 4Å: Chain G: N.121 Chain I: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.201, I:E.202 MG.12: 9 residues within 4Å: Chain C: N.121 Chain K: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.201, K:E.202 MG.14: 9 residues within 4Å: Chain E: N.121 Chain M: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.201, M:E.202 MG.16: 9 residues within 4Å: Chain A: N.121 Chain O: T.171, K.173, K.175, K.199, D.201, E.202, H.292 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.201, O:E.202

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: ACEGIKMO
RubisCO small subunit: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
A

K
C

M
E

O
G

B
B

D
D

F
F

H
H

J
B

L
D

N
F

P
H

RubisCO large subunit

RubisCO small subunit

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