SMTL ID : 1ir2.2 (1 other biounit)

Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 9 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain I: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.6: 8 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, D.203, E.204 Chain K: N.123 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.10: 8 residues within 4Å: Chain E: T.173, K.175, K.177, K.201, D.203, E.204 Chain M: N.123 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.14: 8 residues within 4Å: Chain G: T.173, K.175, K.177, K.201, D.203, E.204 Chain O: N.123 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.18: 8 residues within 4Å: Chain A: N.123 Chain I: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.19 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.22: 8 residues within 4Å: Chain C: N.123 Chain K: T.173, K.175, K.177, K.201, D.203, E.204 Ligands: CAP.23 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.27: 9 residues within 4Å: Chain E: N.123 Chain M: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.28 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.32: 9 residues within 4Å: Chain G: N.123 Chain O: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.33 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.203, O:E.204

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

CAP.2: 23 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain I: E.60, T.65, W.66, N.123 Ligands: MG.1 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain I Hydrogen bonds: A:T.173, A:T.173, A:K.175, A:S.379, A:G.381, A:G.403, A:G.404, I:T.65, I:N.123 Water bridges: A:T.173, A:T.173, A:K.177, A:K.177, A:K.177, A:K.177, A:R.295, A:R.295, A:R.295, A:H.327, A:H.327, A:G.329, A:S.379, A:G.380, A:I.382, A:I.382, A:I.382 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.7: 22 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain K: E.60, T.65, W.66, N.123 Ligands: MG.6 34 PLIP interactions: 32 interactions with chain C, 2 interactions with chain K Hydrogen bonds: C:T.173, C:T.173, C:K.175, C:H.327, C:S.379, C:G.381, C:G.403, C:G.404, K:T.65, K:N.123 Water bridges: C:T.173, C:T.173, C:K.177, C:K.177, C:K.177, C:K.177, C:H.294, C:R.295, C:R.295, C:R.295, C:H.327, C:S.379, C:S.379, C:G.380, C:I.382, C:I.382, C:I.382 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.327, C:K.334, C:K.334 CAP.11: 22 residues within 4Å: Chain E: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain M: E.60, T.65, W.66, N.123 Ligands: MG.10 31 PLIP interactions: 29 interactions with chain E, 2 interactions with chain M Hydrogen bonds: E:T.173, E:K.175, E:S.379, E:G.381, E:G.403, E:G.404, M:T.65, M:N.123 Water bridges: E:T.173, E:T.173, E:K.177, E:K.177, E:K.177, E:K.177, E:H.294, E:R.295, E:R.295, E:R.295, E:H.327, E:S.379, E:S.379, E:G.380, E:I.382, E:G.405 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.15: 23 residues within 4Å: Chain G: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain O: E.60, T.65, W.66, N.123 Ligands: MG.14 31 PLIP interactions: 3 interactions with chain O, 28 interactions with chain G Hydrogen bonds: O:T.65, O:N.123, G:T.173, G:T.173, G:K.175, G:S.379, G:G.381, G:G.403, G:G.404 Water bridges: O:E.60, G:T.173, G:T.173, G:K.177, G:K.177, G:K.177, G:R.295, G:R.295, G:R.295, G:H.327, G:H.327, G:S.379, G:G.380, G:I.382, G:I.382 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.19: 22 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain I: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.18 32 PLIP interactions: 29 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:T.173, I:K.175, I:S.379, I:G.381, I:G.403, I:G.404, A:T.65, A:N.123 Water bridges: I:T.173, I:T.173, I:K.177, I:K.177, I:K.177, I:H.294, I:R.295, I:R.295, I:R.295, I:H.327, I:S.379, I:S.379, I:G.380, I:I.382, I:I.382, I:G.405, A:E.60 Salt bridges: I:K.175, I:K.175, I:K.177, I:R.295, I:H.327, I:K.334, I:K.334 CAP.23: 21 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain K: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.22 32 PLIP interactions: 30 interactions with chain K, 2 interactions with chain C Hydrogen bonds: K:T.173, K:K.175, K:S.379, K:G.381, K:G.403, K:G.404, C:T.65, C:N.123 Water bridges: K:T.173, K:T.173, K:K.177, K:K.177, K:K.177, K:K.177, K:H.294, K:R.295, K:R.295, K:R.295, K:H.327, K:G.329, K:S.379, K:S.379, K:G.380, K:I.382, K:I.382 Salt bridges: K:K.175, K:K.175, K:K.177, K:R.295, K:H.327, K:K.334, K:K.334 CAP.28: 22 residues within 4Å: Chain E: E.60, T.65, W.66, N.123 Chain M: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.27 34 PLIP interactions: 32 interactions with chain M, 2 interactions with chain E Hydrogen bonds: M:T.173, M:K.175, M:H.327, M:S.379, M:G.381, M:G.403, M:G.404, E:T.65, E:N.123 Water bridges: M:T.173, M:T.173, M:K.177, M:K.177, M:K.177, M:K.177, M:H.294, M:R.295, M:R.295, M:R.295, M:H.327, M:G.329, M:S.379, M:S.379, M:G.380, M:I.382, M:I.382, M:G.405 Salt bridges: M:K.175, M:K.175, M:K.177, M:R.295, M:H.327, M:K.334, M:K.334 CAP.33: 22 residues within 4Å: Chain G: E.60, T.65, W.66, N.123 Chain O: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.32 35 PLIP interactions: 32 interactions with chain O, 3 interactions with chain G Hydrogen bonds: O:T.173, O:T.173, O:K.175, O:E.204, O:S.379, O:G.381, O:G.403, O:G.404, G:T.65, G:N.123 Water bridges: O:T.173, O:T.173, O:K.177, O:K.177, O:K.177, O:R.295, O:R.295, O:R.295, O:H.327, O:H.327, O:G.329, O:S.379, O:S.379, O:G.380, O:I.382, O:I.382, O:I.382, G:E.60 Salt bridges: O:K.175, O:K.175, O:K.177, O:R.295, O:H.327, O:K.334, O:K.334

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: L.270, G.273, M.297 Chain I: L.270, M.297, I.301 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: V.149, I.282, R.285, D.286 Chain C: E.249, K.252 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain C: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain C: V.149, I.282, R.285, D.286 Chain E: E.249, K.252 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain E: V.17, K.18, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain E: V.149, I.282, R.285, D.286 Chain G: E.249, K.252 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain G: V.17, K.18, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: K.252 Chain G: V.149, I.282, R.285, D.286 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain I: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain I: V.149, I.282, R.285, D.286 Chain O: E.249, K.252 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain K: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: L.270, I.301 Chain K: L.270, M.297 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain I: E.249, K.252 Chain K: V.149, I.282, R.285, D.286 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain M: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain E: L.270, F.274, I.301 Chain M: L.270, M.297 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain K: E.249, K.252 Chain M: V.149, I.282, R.285, D.286 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain O: V.17, K.18, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain G: L.270, M.297 Chain O: L.270, F.274, I.301 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain M: E.249, K.252 Chain O: V.149, I.282, R.285, D.286 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizohata, E. et al., Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. J.Mol.Biol. (2002)

Release Date

2002-03-20

Peptides

Large subunit of Rubisco: ACEGIKMO
Small subunit of Rubisco: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

E
U

G
V

I
W

K
X

M
Y

O
Z

B
1

D
2

F
3

H
4

J
5

L
6

N
7

P
8

Large subunit of Rubisco

Small subunit of Rubisco

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