SMTL ID : 2vdh.1

CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT C172S MUTATION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-oligomer

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 B: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.9: 7 residues within 4Å: Chain A: N.123 Chain B: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.203, B:E.204 MG.16: 7 residues within 4Å: Chain C: K.175, K.177, K.201, D.203, E.204 Chain D: N.123 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.24: 7 residues within 4Å: Chain C: N.123 Chain D: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.25 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.203, D:E.204 MG.31: 7 residues within 4Å: Chain E: K.175, K.177, K.201, D.203, E.204 Chain F: N.123 Ligands: CAP.32 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.39: 7 residues within 4Å: Chain E: N.123 Chain F: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.40 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.203, F:E.204 MG.47: 7 residues within 4Å: Chain G: K.175, K.177, K.201, D.203, E.204 Chain H: N.123 Ligands: CAP.48 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.54: 7 residues within 4Å: Chain G: N.123 Chain H: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.55 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.203, H: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 B: E.60, T.65, W.66, N.123 Ligands: MG.1 31 PLIP interactions: 28 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.173, A:T.173, A:K.175, A:H.298, A:S.379, A:G.381, A:G.403, A:G.404, B:T.65, B:T.65, B:N.123 Water bridges: A:K.177, A:K.177, A:K.177, A:K.177, A:R.295, A:R.295, A:G.329, A:S.379, A:G.380, A:G.380, A:I.382, A:I.382, A:Q.401 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.10: 21 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain B: 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.9 30 PLIP interactions: 27 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.173, B:K.175, B:E.204, B:H.298, B:S.379, B:G.380, B:G.381, B:G.403, B:G.404, A:T.65, A:T.65, A:N.123 Water bridges: B:T.173, B:T.173, B:K.177, B:K.177, B:K.177, B:K.177, B:R.295, B:G.329, B:I.382, B:I.382, B:I.382 Salt bridges: B:K.175, B:K.175, B:K.177, B:R.295, B:H.327, B:K.334, B:K.334 CAP.17: 21 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, G.403, G.404 Chain D: E.60, T.65, W.66, N.123 Ligands: MG.16 29 PLIP interactions: 26 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.173, C:T.173, C:K.175, C:E.204, C:H.298, C:S.379, C:G.381, C:G.403, C:G.404, D:T.65, D:N.123 Water bridges: C:T.173, C:K.177, C:R.295, C:R.295, C:G.329, C:G.380, C:G.380, C:I.382, C:Q.401, C:G.405, 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.25: 22 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain D: 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.24 30 PLIP interactions: 5 interactions with chain C, 25 interactions with chain D Hydrogen bonds: C:T.65, C:T.65, C:N.123, D:T.173, D:K.175, D:E.204, D:S.379, D:G.381, D:G.403, D:G.404 Water bridges: C:E.60, C:E.60, D:T.173, D:K.177, D:R.295, D:H.298, D:K.334, D:S.379, D:S.379, D:G.380, D:G.380, D:I.382, D:I.382 Salt bridges: D:K.175, D:K.175, D:K.177, D:R.295, D:H.327, D:K.334, D:K.334 CAP.32: 21 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, G.403, G.404 Chain F: E.60, T.65, W.66, N.123 Ligands: MG.31 27 PLIP interactions: 22 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:T.173, E:T.173, E:K.175, E:E.204, E:H.298, E:S.379, E:G.380, E:G.381, E:G.403, E:G.404, F:T.65, F:N.123 Water bridges: E:K.177, E:G.329, E:G.329, E:I.382, E:G.405, F:E.60, F:E.60, F:T.65 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.40: 22 residues within 4Å: Chain E: E.60, T.65, W.66, N.123 Chain F: 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.39 26 PLIP interactions: 22 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:T.173, F:K.175, F:H.298, F:S.379, F:G.381, F:G.403, F:G.404, E:T.65, E:N.123 Water bridges: F:T.173, F:T.173, F:K.177, F:K.177, F:G.329, F:G.380, F:I.382, F:I.382, E:E.60, E:T.65 Salt bridges: F:K.175, F:K.175, F:K.177, F:R.295, F:H.327, F:K.334, F:K.334 CAP.48: 22 residues within 4Å: Chain G: 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 H: E.60, T.65, W.66, N.123 Ligands: MG.47 28 PLIP interactions: 25 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:T.173, G:T.173, G:K.175, G:E.204, G:H.298, G:S.379, G:G.381, G:G.403, G:G.404, H:T.65, H:N.123 Water bridges: G:T.173, G:K.177, G:K.177, G:K.177, G:G.329, G:S.379, G:I.382, G:I.382, G:G.405, H:T.65 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.55: 23 residues within 4Å: Chain G: E.60, T.65, W.66, N.123 Chain H: 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.54 33 PLIP interactions: 29 interactions with chain H, 4 interactions with chain G Hydrogen bonds: H:T.173, H:K.175, H:D.203, H:D.203, H:H.298, H:S.379, H:G.381, H:G.403, H:G.404, G:T.65, G:T.65, G:N.123 Water bridges: H:T.173, H:K.177, H:K.177, H:K.177, H:R.295, H:R.295, H:R.295, H:G.329, H:S.379, H:G.380, H:G.380, H:I.382, H:G.405, G:E.60 Salt bridges: H:K.175, H:K.175, H:K.177, H:R.295, H:H.327, H:K.334, H:K.334

57 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: G.64, T.65, T.67, T.68, V.69, D.72 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.20, E.52, A.129 Chain B: F.469 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: H.310, F.311, E.336, G.337, E.338, V.341, F.345, D.473 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: K.466, F.467, E.468, F.469 Ligands: EDO.13 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: L.270 Chain B: L.270 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: F.469 Chain B: Y.20, E.52, A.129 Ligands: EDO.7 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: R.295, E.336, G.337, V.341, F.345, D.473 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: Y.24, T.68, V.69, D.72, L.77 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 10 residues within 4Å: Chain C: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: Y.20, E.52 Chain D: F.469 Ligands: EDO.28 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: L.270, G.273 Chain D: L.270 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: R.295, H.298, F.311, E.336, V.341, F.345, D.473 Ligand excluded by PLIP EDO.26: 10 residues within 4Å: Chain D: G.16, V.17, K.18, D.19, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.29 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: F.469 Chain D: Y.20, E.52 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain D: K.466, F.467, E.468, F.469 Ligands: EDO.20 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain D: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.26 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: R.295, E.336, G.337, F.345, D.473 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain E: L.270 Chain F: L.270 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain E: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.35 Ligand excluded by PLIP EDO.35: 10 residues within 4Å: Chain E: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligands: EDO.34 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain E: Y.20, E.52, A.129 Chain F: F.469 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain E: R.295, S.328, E.336, F.345, D.473 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain F: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.42 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain F: G.16, V.17, K.18, T.65, W.66, T.67, T.68 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain F: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain F: R.295, H.298, F.311, S.328, G.329, E.336, F.345, D.473 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain F: D.19, Y.20, E.52, A.129 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain F: Y.226, K.227, A.230 Chain P: K.49, E.55, D.69, N.70 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain G: Y.24, G.64, T.68, V.69, D.72, L.77 Ligand excluded by PLIP EDO.50: 9 residues within 4Å: Chain G: G.16, V.17, K.18, D.19, Y.20, T.65, W.66, T.67, T.68 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain G: R.295, F.311, S.328, G.329, E.336, F.345, D.473 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain G: Y.20, V.48, E.52, A.129 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain G: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain H: Y.24, T.68, V.69, D.72, L.77 Ligands: EDO.57 Ligand excluded by PLIP EDO.57: 10 residues within 4Å: Chain H: G.16, V.17, K.18, D.19, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.56 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain G: F.469 Chain H: Y.20, E.52, A.129 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain H: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain H: R.295, E.336, F.345, D.473 Ligand excluded by PLIP EDO.61: 2 residues within 4Å: Chain G: L.270 Chain H: L.270 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain C: Y.226, K.227 Chain I: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.63: 8 residues within 4Å: Chain H: Y.226, K.227, A.230 Chain J: K.49, E.55, S.56, D.69, N.70 Ligand excluded by PLIP EDO.64: 7 residues within 4Å: Chain J: G.37, W.38, I.39, M.80, F.81, G.82, C.83 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain K: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP EDO.66: 7 residues within 4Å: Chain E: Y.226, K.227, A.230 Chain K: K.49, E.55, D.69, N.70 Ligand excluded by PLIP EDO.67: 7 residues within 4Å: Chain B: Y.226, K.227, A.230 Chain L: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain M: G.37, W.38, I.39, F.81, G.82 Ligand excluded by PLIP EDO.69: 7 residues within 4Å: Chain G: Y.226, K.227, A.230 Chain M: K.49, E.55, D.69, N.70 Ligand excluded by PLIP EDO.70: 8 residues within 4Å: Chain D: Y.226, K.227, A.230 Chain N: K.49, E.55, S.56, D.69, N.70 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain N: G.37, W.38, I.39, G.82, C.83 Ligand excluded by PLIP EDO.72: 8 residues within 4Å: Chain A: Y.226, K.227, A.230 Chain O: K.49, E.55, S.56, D.69, N.70 Ligand excluded by PLIP EDO.73: 6 residues within 4Å: Chain O: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Murria, M.-J. et al., Structural and Functional Consequences of the Replacement of Proximal Residues Cys-172 and Cys-192 in the Large Subunit of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Chlamydomonas Reinhardtii. Biochem.J. (2008)

Release Date

2008-11-04

Peptides

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN: ABCDEFGH
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1: 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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1

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