SMTL ID : 7qt1.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 K: E.53, T.58, W.59, N.109 Ligands: MG.2 33 PLIP interactions: 30 interactions with chain A, 3 interactions with chain K Hydrogen bonds: A:T.159, A:T.159, A:K.161, A:D.189, A:S.365, A:G.367, A:G.389, A:G.390, K:T.58, K:T.58, K:N.109 Water bridges: A:T.159, A:K.163, A:K.163, A:K.163, A:K.163, A:R.281, A:R.281, A:R.281, A:H.284, A:G.315, A:S.365, A:G.366, A:I.368, 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 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 I: E.53, T.58, W.59, N.109 Ligands: MG.4 31 PLIP interactions: 29 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:T.159, C:K.161, C:G.367, C:G.389, C:G.390, I:T.58, I:N.109 Water bridges: C:T.159, 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.284, C:H.313, C:G.315, C:S.365, 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.5: 21 residues within 4Å: Chain E: 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 O: E.53, T.58, W.59, N.109 Ligands: MG.6 32 PLIP interactions: 29 interactions with chain E, 3 interactions with chain O Hydrogen bonds: E:T.159, E:T.159, E:K.161, E:G.367, E:G.389, E:G.390, O:T.58, O:T.58, O:N.109 Water bridges: E:T.159, E:T.159, E:K.163, E:K.163, E:K.163, E:K.163, E:H.280, E:R.281, E:R.281, E:H.284, E:H.313, E:G.315, E:S.365, E:G.366, E:G.391, 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.7: 21 residues within 4Å: 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 Chain M: E.53, T.58, W.59, N.109 Ligands: MG.8 32 PLIP interactions: 28 interactions with chain G, 4 interactions with chain M Hydrogen bonds: G:T.159, G:T.159, G:K.161, G:E.190, G:S.365, G:G.367, G:G.389, G:G.390, M:T.58, M:T.58, M:N.109 Water bridges: G:K.163, G:K.163, G:K.163, G:R.281, G:R.281, G:R.281, G:R.281, G:H.284, G:G.315, G:S.365, G:I.368, G:L.387, G:G.391, M:E.53 Salt bridges: G:K.161, G:K.161, G:K.163, G:R.281, G:H.313, G:K.320, G:K.320 CAP.9: 21 residues within 4Å: Chain C: E.53, T.58, W.59, N.109 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 Ligands: MG.10 33 PLIP interactions: 30 interactions with chain I, 3 interactions with chain C Hydrogen bonds: I:T.159, I:K.161, I:D.189, I:S.365, I:G.367, I:G.389, I:G.390, C:T.58, C:T.58, C:N.109 Water bridges: I:T.159, I:T.159, I:K.163, I:K.163, I:K.163, I:K.163, I:R.281, I:R.281, I:R.281, I:H.284, I:G.315, I:S.365, I:G.366, I:I.368, 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.11: 21 residues within 4Å: Chain A: E.53, T.58, W.59, N.109 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 Ligands: MG.12 31 PLIP interactions: 3 interactions with chain A, 28 interactions with chain K Hydrogen bonds: A:T.58, A:N.109, K:T.159, K:T.159, K:K.161, K:G.367, K:G.389, K:G.390 Water bridges: A:E.53, K:T.159, K:K.163, K:K.163, K:K.163, K:H.280, K:R.281, K:R.281, K:H.284, K:H.313, K:G.315, K:S.365, K:S.365, K:G.366, K:I.368, K:G.391 Salt bridges: K:K.161, K:K.161, K:K.163, K:R.281, K:H.313, K:K.320, K:K.320 CAP.13: 21 residues within 4Å: Chain G: E.53, T.58, W.59, N.109 Chain M: 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 31 PLIP interactions: 27 interactions with chain M, 4 interactions with chain G Hydrogen bonds: M:T.159, M:K.161, M:G.367, M:G.389, M:G.390, G:T.58, G:T.58, G:N.109 Water bridges: M:T.159, M:T.159, M:K.163, M:K.163, M:K.163, M:H.280, M:R.281, M:R.281, M:H.284, M:H.313, M:G.315, M:S.365, M:G.366, M:G.391, M:G.391, G:E.53 Salt bridges: M:K.161, M:K.161, M:K.163, M:R.281, M:H.313, M:K.320, M:K.320 CAP.15: 21 residues within 4Å: Chain E: E.53, T.58, W.59, N.109 Chain O: 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.16 32 PLIP interactions: 29 interactions with chain O, 3 interactions with chain E Hydrogen bonds: O:T.159, O:K.161, O:D.189, O:S.365, O:G.367, O:G.389, O:G.390, E:T.58, E:T.58, E:N.109 Water bridges: O:T.159, O:K.163, O:K.163, O:K.163, O:K.163, O:R.281, O:R.281, O:R.281, O:R.281, O:H.284, O:G.315, O:S.365, O:I.368, O:L.387, O:G.391 Salt bridges: O:K.161, O:K.161, O:K.163, O:R.281, O:H.313, O:K.320, O: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 K: 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 C: K.161, K.163, K.187, D.189, E.190 Chain I: N.109 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.189, C:E.190 MG.6: 7 residues within 4Å: Chain E: K.161, K.163, K.187, D.189, E.190 Chain O: N.109 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.189, E:E.190 MG.8: 7 residues within 4Å: Chain G: K.161, K.163, K.187, D.189, E.190 Chain M: N.109 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.189, G:E.190 MG.10: 8 residues within 4Å: Chain C: N.109 Chain I: T.159, K.161, K.163, K.187, D.189, E.190 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.189, I:E.190 MG.12: 7 residues within 4Å: Chain A: N.109 Chain K: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.189, K:E.190 MG.14: 7 residues within 4Å: Chain G: N.109 Chain M: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.189, M:E.190 MG.16: 7 residues within 4Å: Chain E: N.109 Chain O: K.161, K.163, K.187, D.189, E.190 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.189, O: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: 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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