SMTL ID : 9ck5.1

Anthoceros agrestis Rubisco assembled with RbcX1, RbcX2, Raf1, Raf2 and BSD2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.201, D.203, E.204 Ligands: CAP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.204 MG.3: 3 residues within 4Å: Chain B: K.201, E.204 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.204, B:E.204 MG.5: 3 residues within 4Å: Chain C: K.201, E.204 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.204, C:E.204 MG.7: 3 residues within 4Å: Chain D: K.201, E.204 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.204, D:E.204 MG.9: 3 residues within 4Å: Chain E: K.201, E.204 Ligands: CAP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.204 MG.11: 4 residues within 4Å: Chain F: K.201, D.203, E.204 Ligands: CAP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.204 MG.13: 4 residues within 4Å: Chain G: K.201, D.203, E.204 Ligands: CAP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.204 MG.15: 4 residues within 4Å: Chain H: K.201, D.203, E.204 Ligands: CAP.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.204

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

CAP.2: 18 residues within 4Å: Chain A: K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain B: T.65, W.66, N.123 Ligands: MG.1 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.175, A:S.379, A:G.381, A:G.403, A:G.404, B:T.65, B:T.65, B:N.123 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.4: 17 residues within 4Å: Chain A: T.65, W.66, N.123 Chain B: K.175, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.3 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.175, B:S.379, B:G.381, B:G.403, B:G.404, A:T.65, A:T.65 Salt bridges: B:K.175, B:K.175, B:K.177, B:R.295, B:H.327, B:K.334, B:K.334 CAP.6: 17 residues within 4Å: Chain C: K.175, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain D: T.65, W.66, N.123 Ligands: MG.5 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.175, C:S.379, C:G.381, C:G.403, C:G.404, D:T.65, D:T.65 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.327, C:K.334, C:K.334 CAP.8: 18 residues within 4Å: Chain C: T.65, W.66, N.123 Chain D: K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.7 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.175, D:S.379, D:G.381, D:G.403, D:G.404, C:T.65, C:T.65, C:N.123 Salt bridges: D:K.175, D:K.175, D:K.177, D:R.295, D:H.327, D:K.334, D:K.334 CAP.10: 18 residues within 4Å: Chain E: K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain F: T.65, W.66, N.123 Ligands: MG.9 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:K.175, E:S.379, E:G.381, E:G.403, E:G.404, F:T.65, F:T.65, F:N.123 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.12: 18 residues within 4Å: Chain E: T.65, W.66, N.123 Chain F: K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.11 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:T.65, E:T.65, E:N.123, F:K.175, F:S.379, F:G.381, F:G.403, F:G.404 Salt bridges: F:K.175, F:K.175, F:K.177, F:R.295, F:H.327, F:K.334, F:K.334 CAP.14: 18 residues within 4Å: Chain G: K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain H: T.65, W.66, N.123 Ligands: MG.13 15 PLIP interactions: 12 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:K.175, G:S.379, G:G.381, G:G.403, G:G.404, H:T.65, H:T.65, H:N.123 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.16: 17 residues within 4Å: Chain G: T.65, W.66, N.123 Chain H: K.175, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.15 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:K.175, H:E.204, H:S.379, H:G.380, H:G.381, H:G.403, H:G.404, G:T.65, G:T.65, G:N.123 Salt bridges: H:K.175, H:K.175, H:K.177, H:R.295, H:H.327, H:K.334, H:K.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, Z.G. et al., Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems. Mol Plant (2024)

Release Date

2024-11-13

Peptides

RuBisCO large subunit: ABCDEFGH
RuBisCO small subunit: IJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

RuBisCO large subunit

RuBisCO small subunit

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