SMTL ID : 3axm.1

Structure of rice Rubisco in complex with 6PG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.177, K.201, D.203, E.204 Ligands: 6PG.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:E.204, H2O.10 MG.3: 4 residues within 4Å: Chain C: K.201, D.203, E.204 Ligands: 6PG.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:E.204, H2O.27 MG.5: 5 residues within 4Å: Chain E: K.177, K.201, D.203, E.204 Ligands: 6PG.6 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:E.204, H2O.34 MG.7: 4 residues within 4Å: Chain G: K.201, D.203, E.204 Ligands: 6PG.8 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.203, G:E.204, H2O.63 MG.9: 4 residues within 4Å: Chain I: K.201, D.203, E.204 Ligands: 6PG.10 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.203, I:E.204, H2O.76 MG.11: 4 residues within 4Å: Chain K: K.201, D.203, E.204 Ligands: 6PG.12 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.203, K:E.204, H2O.97 MG.13: 4 residues within 4Å: Chain M: K.201, D.203, E.204 Ligands: 6PG.14 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.203, M:E.204, H2O.111 MG.15: 4 residues within 4Å: Chain O: K.201, D.203, E.204 Ligands: 6PG.16 3 PLIP interactions: 2 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:D.203, O:E.204, H2O.133

8 x 6PG: 6-PHOSPHOGLUCONIC ACID(Non-covalent)

6PG.2: 12 residues within 4Å: Chain A: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, G.329, S.379 Chain C: N.123 Ligands: MG.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C Water bridges: A:T.173, A:K.175, A:K.177, A:K.177, A:K.177, A:H.294, A:R.295, A:R.295, A:H.298, A:H.298, A:H.327, A:S.379, A:G.380, A:G.403 Salt bridges: A:K.175, A:R.295, A:H.298 Hydrogen bonds: C:N.123, C:N.123 6PG.4: 13 residues within 4Å: Chain A: N.123 Chain C: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, G.329, S.379, G.380 Ligands: MG.3 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.379, A:N.123, A:N.123 Water bridges: C:T.173, C:K.175, C:K.177, C:K.177, C:K.177, C:H.294, C:R.295, C:H.298, C:H.327, C:H.327, C:S.379, C:S.379, C:G.380, C:G.380, C:G.380, C:G.403 Salt bridges: C:K.175, C:K.177, C:R.295, C:H.298 6PG.6: 13 residues within 4Å: Chain E: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, S.379, G.380 Chain G: N.123 Ligands: MG.5 20 PLIP interactions: 2 interactions with chain G, 18 interactions with chain E Hydrogen bonds: G:N.123, G:N.123, E:H.327, E:S.379 Water bridges: E:T.173, E:K.175, E:K.175, E:K.177, E:K.177, E:H.294, E:R.295, E:H.298, E:S.379, E:S.379, E:G.380, E:G.380 Salt bridges: E:K.175, E:K.177, E:R.295, E:H.298 6PG.8: 12 residues within 4Å: Chain E: N.123 Chain G: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, G.329, S.379 Ligands: MG.7 19 PLIP interactions: 2 interactions with chain E, 17 interactions with chain G Hydrogen bonds: E:N.123, E:N.123, G:H.327, G:S.379 Water bridges: G:T.173, G:K.175, G:K.177, G:H.294, G:R.295, G:H.298, G:S.379, G:S.379, G:G.380, G:G.380, G:G.403 Salt bridges: G:K.175, G:K.177, G:R.295, G:H.298 6PG.10: 12 residues within 4Å: Chain I: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, S.379, G.380 Chain K: N.123 Ligands: MG.9 20 PLIP interactions: 17 interactions with chain I, 3 interactions with chain K Hydrogen bonds: I:S.379, I:G.380, K:N.123, K:N.123 Water bridges: I:T.173, I:T.173, I:K.175, I:K.177, I:H.294, I:H.298, I:A.299, I:G.329, I:G.329, I:S.379, I:G.380, I:G.403, K:G.122 Salt bridges: I:K.175, I:R.295, I:H.298 6PG.12: 14 residues within 4Å: Chain I: N.123 Chain K: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380 Ligands: MG.11 21 PLIP interactions: 19 interactions with chain K, 2 interactions with chain I Hydrogen bonds: K:S.379, I:N.123, I:N.123 Water bridges: K:T.173, K:T.173, K:K.175, K:K.177, K:K.177, K:K.177, K:H.294, K:R.295, K:H.298, K:H.327, K:S.379, K:S.379, K:G.380, K:G.403 Salt bridges: K:K.175, K:K.177, K:R.295, K:H.298 6PG.14: 12 residues within 4Å: Chain M: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, G.329, S.379 Chain O: N.123 Ligands: MG.13 20 PLIP interactions: 17 interactions with chain M, 3 interactions with chain O Hydrogen bonds: M:S.379, O:N.123, O:N.123 Water bridges: M:T.173, M:K.175, M:K.177, M:K.177, M:H.298, M:H.298, M:G.329, M:G.329, M:G.329, M:G.380, M:G.380, M:G.403, O:G.122 Salt bridges: M:K.175, M:K.177, M:R.295, M:H.298 6PG.16: 13 residues within 4Å: Chain M: N.123 Chain O: T.173, K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379 Ligands: MG.15 19 PLIP interactions: 16 interactions with chain O, 3 interactions with chain M Hydrogen bonds: O:S.379, M:N.123, M:N.123 Water bridges: O:T.173, O:K.175, O:K.177, O:K.177, O:H.294, O:R.295, O:H.298, O:H.327, O:G.329, O:G.329, O:G.380, O:G.403, M:G.64 Salt bridges: O:K.175, O:R.295, O:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumura, H. et al., Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate. J.Mol.Biol. (2012)

Release Date

2012-04-11

Peptides

Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain, chloroplastic: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
E

K
F

M
G

O
H

B
S

D
T

F
U

H
V

J
W

L
X

N
Y

P
Z

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain, chloroplastic

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