SMTL ID : 8qmw.1

Non-obligately L8S8-complex forming RubisCO derived from ancestral sequence reconstruction and rational engineering in L8S8 complex with substitutions R269W, E271R, L273N

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-8-8-mer

Ligands

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

CAP.1: 21 residues within 4Å: Chain A: 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 B: E.53, T.58, W.59, N.109 Ligands: MG.2 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.159, A:T.159, A:K.161, A:G.367, A:G.389, A:G.390, B:T.58, B:N.109 Water bridges: A:T.159, A:K.163, A:K.163, A:K.163, A:H.280, A:R.281, A:R.281, A:H.313, A:G.315, A:K.320, A:S.365, A:G.366, A:G.366, A:I.368, A:G.391 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: 21 residues within 4Å: Chain A: E.53, T.58, W.59, N.109 Chain B: 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.4 30 PLIP interactions: 3 interactions with chain A, 27 interactions with chain B Hydrogen bonds: A:T.58, A:N.109, B:T.159, B:K.161, B:E.190, B:G.367, B:G.389, B:G.390 Water bridges: A:E.53, B:T.159, B:T.159, B:K.163, B:K.163, B:H.280, B:R.281, B:R.281, B:H.313, B:G.315, B:K.320, B:S.365, B:S.365, B:G.366, 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 D: E.53, T.58, W.59, N.109 Ligands: MG.6 32 PLIP interactions: 29 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.159, C:K.161, C:E.190, C:G.367, C:G.389, C:G.390, D:T.58, D:T.58, D:N.109 Water bridges: C:T.159, C:T.159, C:K.163, C:K.163, C:K.163, C:K.163, C:R.281, C:R.281, C:H.313, C:H.313, C:G.315, 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.8: 21 residues within 4Å: Chain C: E.53, T.58, W.59, N.109 Chain D: 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.9 30 PLIP interactions: 27 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.159, D:T.159, D:K.161, D:G.367, D:G.389, D:G.390, C:T.58, C:N.109 Water bridges: D:T.159, D:K.163, D:K.163, D:K.163, D:H.280, D:R.281, D:R.281, D:H.313, D:G.315, D:S.365, D:S.365, D:I.368, D:L.387, D:G.391, C:T.58 Salt bridges: D:K.161, D:K.161, D:K.163, D:R.281, D:H.313, D:K.320, D:K.320 CAP.10: 21 residues within 4Å: Chain I: 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 J: E.53, T.58, W.59, N.109 Ligands: MG.11 31 PLIP interactions: 28 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:T.159, I:K.161, I:G.367, I:G.389, I:G.390, J:T.58, J:T.58, J:N.109 Water bridges: I:T.159, I:T.159, I:K.163, I:K.163, I:K.163, I:H.280, I:R.281, I:R.281, I:H.313, I:G.315, I:K.320, I:S.365, I:G.366, I:G.366, I:I.368, I:G.391 Salt bridges: I:K.161, I:K.161, I:K.163, I:R.281, I:H.313, I:K.320, I:K.320 CAP.12: 21 residues within 4Å: Chain I: E.53, T.58, W.59, N.109 Chain J: 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.13 28 PLIP interactions: 2 interactions with chain I, 26 interactions with chain J Hydrogen bonds: I:N.109, J:T.159, J:T.159, J:K.161, J:E.190, J:G.367, J:G.389, J:G.390 Water bridges: I:T.58, J:T.159, J:K.163, J:K.163, J:H.280, J:R.281, J:R.281, J:G.315, J:K.320, J:S.365, J:S.365, J:G.366, J:G.391 Salt bridges: J:K.161, J:K.161, J:K.163, J:R.281, J:H.313, J:K.320, J:K.320 CAP.14: 21 residues within 4Å: Chain K: 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 L: E.53, T.58, W.59, N.109 Ligands: MG.15 32 PLIP interactions: 29 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:T.159, K:T.159, K:K.161, K:E.190, K:G.367, K:G.389, K:G.390, L:T.58, L:N.109 Water bridges: K:T.159, K:K.163, K:K.163, K:K.163, K:H.280, K:R.281, K:R.281, K:H.313, K:G.315, K:G.315, K:S.365, K:G.366, K:I.368, K:L.387, K:G.391, L:T.58 Salt bridges: K:K.161, K:K.161, K:K.163, K:R.281, K:H.313, K:K.320, K:K.320 CAP.17: 21 residues within 4Å: Chain K: E.53, T.58, W.59, N.109 Chain L: 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.18 31 PLIP interactions: 27 interactions with chain L, 4 interactions with chain K Hydrogen bonds: L:T.159, L:K.161, L:G.367, L:G.389, L:G.390, K:T.58, K:T.58, K:N.109 Water bridges: L:T.159, L:T.159, L:K.163, L:K.163, L:K.163, L:H.280, L:R.281, L:R.281, L:H.313, L:G.315, L:S.365, L:S.365, L:I.368, L:L.387, L:G.391, K:E.53 Salt bridges: L:K.161, L:K.161, L:K.163, L:R.281, L:H.313, L:K.320, L:K.320

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.161, K.163, K.187, D.189, E.190 Chain B: 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 A: N.109 Chain B: K.161, K.163, K.187, D.189, E.190 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: K.161, K.163, K.187, D.189, E.190 Chain D: N.109 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.189, C:E.190 MG.9: 8 residues within 4Å: Chain C: N.109 Chain D: K.161, K.163, K.187, D.189, E.190, H.280 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.189, D:E.190 MG.11: 7 residues within 4Å: Chain I: K.161, K.163, K.187, D.189, E.190 Chain J: N.109 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.189, I:E.190 MG.13: 7 residues within 4Å: Chain I: N.109 Chain J: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.189, J:E.190 MG.15: 7 residues within 4Å: Chain K: K.161, K.163, K.187, D.189, E.190 Chain L: N.109 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.189, K:E.190 MG.18: 8 residues within 4Å: Chain K: N.109 Chain L: K.161, K.163, K.187, D.189, E.190, H.280 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.189, L:E.190

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.7: 4 residues within 4Å: Chain C: P.291, E.322, G.323, D.324 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.323, C:D.324, C:D.324, C:R.325, C:A.326 B3P.16: 4 residues within 4Å: Chain K: P.291, E.322, G.323, D.324 5 PLIP interactions: 5 interactions with chain K Water bridges: K:G.323, K:D.324, K:D.324, K:R.325, K:A.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, L. et al., Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes. Embo J. (2025)

Release Date

2024-10-02

Peptides

RubisCO large subunit: ABCDIJKL
RubisCO small subunit: EFGHMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

I
A

J
B

K
C

L
D

E
E

F
F

G
G

H
H

M
E

N
F

O
G

P
H

RubisCO large subunit

RubisCO small subunit

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