SMTL ID : 3zxw.1

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.175, K.177, K.201, D.203, E.204 Chain M: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.7: 8 residues within 4Å: Chain C: K.175, K.177, K.201, D.203, E.204, H.294 Chain K: N.123 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.13: 7 residues within 4Å: Chain E: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.17: 8 residues within 4Å: Chain G: K.175, K.177, K.201, D.203, E.204, H.294 Chain O: N.123 Ligands: CAP.18 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.20: 7 residues within 4Å: Chain E: N.123 Chain I: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.21 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.26: 8 residues within 4Å: Chain C: N.123 Chain K: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.27 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.32: 7 residues within 4Å: Chain M: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.33 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.36: 8 residues within 4Å: Chain G: N.123 Chain O: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.37 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: 22 residues within 4Å: Chain A: 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.1 31 PLIP interactions: 28 interactions with chain A, 3 interactions with chain M Hydrogen bonds: A:T.173, A:K.175, A:E.204, A:G.381, A:G.403, A:G.404, M:T.65, M:T.65, M:N.123 Water bridges: A:T.173, A:K.177, A:K.177, A:K.177, A:K.177, A:H.294, A:R.295, A:R.295, A:R.295, A:H.327, A:G.329, A:S.379, A:I.382, A:I.382, A:G.405 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.8: 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.7 28 PLIP interactions: 2 interactions with chain K, 26 interactions with chain C Hydrogen bonds: K:T.65, K:N.123, C:T.173, C:K.175, C:H.298, C:S.379, C:G.381, C:G.403, C:G.404 Water bridges: C:T.173, C:K.177, C:K.177, C:K.177, C:K.177, C:R.295, C:R.295, C:G.329, C:G.380, C:G.380, C:I.382, C:G.405 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.327, C:K.334, C:K.334 CAP.14: 23 residues within 4Å: Chain E: 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.13 27 PLIP interactions: 24 interactions with chain E, 3 interactions with chain I Hydrogen bonds: E:T.173, E:K.175, E:G.381, E:G.403, E:G.404, I:T.65, I:T.65, I:N.123 Water bridges: E:K.177, E:K.177, E:H.294, E:R.295, E:R.295, E:H.327, E:G.329, E:G.329, 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.18: 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.17 29 PLIP interactions: 26 interactions with chain G, 3 interactions with chain O Hydrogen bonds: G:T.173, G:K.175, G:E.204, G:H.298, G:S.379, G:G.381, G:G.403, G:G.404, O:T.65, O:N.123 Water bridges: G:K.177, G:K.177, G:K.177, G:R.295, G:R.295, G:R.295, G:G.329, G:G.329, G:G.380, G:I.382, G:G.405, O:E.60 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.21: 22 residues within 4Å: Chain E: 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.20 29 PLIP interactions: 3 interactions with chain E, 26 interactions with chain I Hydrogen bonds: E:T.65, E:N.123, I:T.173, I:T.173, I:K.175, I:E.204, I:G.381, I:G.403, I:G.404 Water bridges: E:T.65, I:K.177, I:K.177, I:K.177, I:H.294, I:R.295, I:R.295, I:R.295, I:G.329, I:S.379, I:I.382, I:I.382, I:G.405 Salt bridges: I:K.175, I:K.175, I:K.177, I:R.295, I:H.327, I:K.334, I:K.334 CAP.27: 22 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, F.402, G.403, G.404 Ligands: MG.26 27 PLIP interactions: 26 interactions with chain K, 1 interactions with chain C Hydrogen bonds: K:T.173, K:T.173, K:K.175, K:H.298, K:S.379, K:G.381, K:G.403, K:G.404, C:N.123 Water bridges: K:K.177, K:K.177, K:K.177, K:K.177, K:R.295, K:R.295, K:G.329, K:G.380, K:G.380, K:I.382, K:G.405 Salt bridges: K:K.175, K:K.175, K:K.177, K:R.295, K:H.327, K:K.334, K:K.334 CAP.33: 23 residues within 4Å: Chain A: 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.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.32 27 PLIP interactions: 24 interactions with chain M, 3 interactions with chain A Hydrogen bonds: M:T.173, M:T.173, M:K.175, M:G.381, M:G.403, M:G.404, A:T.65, A:T.65, A:N.123 Water bridges: M:K.177, M:K.177, M:H.294, M:R.295, M:R.295, M:G.329, M:G.329, M:S.379, M:G.380, 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.37: 23 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.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.36 30 PLIP interactions: 28 interactions with chain O, 2 interactions with chain G Hydrogen bonds: O:T.173, O:T.173, O:K.175, O:D.203, O:E.204, O:H.298, O:S.379, O:G.381, O:G.403, O:G.404, G:N.123 Water bridges: O:K.177, O:K.177, O:K.177, O:R.295, O:R.295, O:R.295, O:G.329, O:G.329, O:G.380, O:I.382, O:G.405, G:T.65 Salt bridges: O:K.175, O:K.175, O:K.177, O:R.295, O:H.327, O:K.334, O:K.334

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: R.295, H.298, D.302, T.328, E.336, F.345, D.473 Ligand excluded by PLIP GOL.5: 2 residues within 4Å: Chain A: E.88, R.358 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: R.215, F.256, E.259 Chain G: D.286, N.287 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain C: K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain C: D.86, I.87, E.88 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain C: K.258, E.261, M.262, P.263, M.289 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain E: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain E: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain G: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain I: K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain I: R.295, H.298, D.302, T.328, E.336, F.345, D.473 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain I: E.88, R.358 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain I: R.215, F.256, E.259 Chain O: D.286, N.287 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain K: K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain K: D.86, I.87, E.88 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain K: K.258, E.261, M.262, P.263, M.289 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain K: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP GOL.34: 9 residues within 4Å: Chain M: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain M: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain O: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terlecka, B. et al., Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus. To be Published

Release Date

2012-08-29

Peptides

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN: ACEGIKMO
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN: 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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

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