SMTL ID : 1gk8.1

Rubisco from Chlamydomonas reinhardtii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: 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.10: 9 residues within 4Å: Chain B: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain L: N.123 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.203, B:E.204 MG.17: 9 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain K: N.123 Ligands: CAP.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.26: 9 residues within 4Å: Chain D: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain J: N.123 Ligands: CAP.27 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.203, D:E.204 MG.42: 8 residues within 4Å: Chain A: N.123 Chain I: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.43 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.51: 9 residues within 4Å: Chain D: N.123 Chain J: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.52 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.203, J:E.204 MG.58: 9 residues within 4Å: Chain C: N.123 Chain K: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.59 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.67: 9 residues within 4Å: Chain B: N.123 Chain L: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.68 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.203, L:E.204

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

CAP.2: 21 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, G.403, G.404 Chain I: E.60, T.65, W.66, N.123 Ligands: MG.1 34 PLIP interactions: 31 interactions with chain A, 3 interactions with chain I Hydrogen bonds: A:T.173, A:T.173, A:K.175, A:S.379, 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:R.295, A:R.295, A:R.295, A:R.295, A:H.298, A:G.329, A:S.379, A:G.380, A:I.382, A:I.382, A:G.405, I:T.65 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.11: 21 residues within 4Å: 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 Chain L: E.60, T.65, W.66, N.123 Ligands: MG.10 34 PLIP interactions: 31 interactions with chain B, 3 interactions with chain L Hydrogen bonds: B:T.173, B:T.173, B:K.175, B:S.379, B:S.379, B:G.381, B:G.403, B:G.404, L:T.65, L:N.123 Water bridges: B:T.173, B:T.173, B:K.177, B:K.177, B:K.177, B:R.295, B:R.295, B:R.295, B:R.295, B:H.298, B:G.329, B:G.329, B:G.380, B:I.382, B:I.382, B:G.405, L: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.18: 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 K: E.60, T.65, W.66, N.123 Ligands: MG.17 33 PLIP interactions: 30 interactions with chain C, 3 interactions with chain K Hydrogen bonds: C:T.173, C:T.173, C:K.175, C:H.298, C:S.379, 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:R.295, C:R.295, C:R.295, C:G.329, C:S.379, C:G.380, C:I.382, C:I.382, C:G.405, K: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.27: 21 residues within 4Å: 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, G.403, G.404 Chain J: E.60, T.65, W.66, N.123 Ligands: MG.26 32 PLIP interactions: 29 interactions with chain D, 3 interactions with chain J Hydrogen bonds: D:T.173, D:T.173, D:K.175, D:H.298, D:S.379, D:S.379, D:G.381, D:G.403, D:G.404, J:T.65, J:N.123 Water bridges: D:K.177, D:K.177, D:K.177, D:R.295, D:R.295, D:R.295, D:G.329, D:G.329, D:G.380, D:I.382, D:I.382, D:Q.401, D:G.405, J:T.65 Salt bridges: D:K.175, D:K.175, D:K.177, D:R.295, D:H.327, D:K.334, D:K.334 CAP.43: 21 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, G.403, G.404 Ligands: MG.42 34 PLIP interactions: 31 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:T.173, I:K.175, I:S.379, I:S.379, I:G.381, I:G.403, I:G.404, A:T.65, A:T.65, A:N.123 Water bridges: I:T.173, I:T.173, I:K.177, I:K.177, I:K.177, I:K.177, I:R.295, I:R.295, I:R.295, I:R.295, I:H.298, I:G.329, I:S.379, I:G.380, 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.52: 21 residues within 4Å: Chain D: E.60, T.65, W.66, N.123 Chain J: 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.51 34 PLIP interactions: 31 interactions with chain J, 3 interactions with chain D Hydrogen bonds: J:T.173, J:K.175, J:S.379, J:S.379, J:G.381, J:G.403, J:G.404, D:T.65, D:T.65, D:N.123 Water bridges: J:T.173, J:T.173, J:K.177, J:K.177, J:K.177, J:K.177, J:R.295, J:R.295, J:R.295, J:R.295, J:H.298, J:G.329, J:G.329, J:G.380, J:I.382, J:I.382, J:G.405 Salt bridges: J:K.175, J:K.175, J:K.177, J:R.295, J:H.327, J:K.334, J:K.334 CAP.59: 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.58 33 PLIP interactions: 30 interactions with chain K, 3 interactions with chain C Hydrogen bonds: K:T.173, K:K.175, K:H.298, K:S.379, K:S.379, K:G.381, K:G.403, K:G.404, C:T.65, 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:R.295, K:R.295, K:R.295, K:G.329, K:S.379, K:G.380, K:I.382, 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.68: 21 residues within 4Å: Chain B: E.60, T.65, W.66, N.123 Chain L: 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.67 33 PLIP interactions: 30 interactions with chain L, 3 interactions with chain B Hydrogen bonds: L:T.173, L:K.175, L:H.298, L:S.379, L:S.379, L:G.381, L:G.403, L:G.404, B:T.65, B:T.65, B:N.123 Water bridges: L:T.173, L:K.177, L:K.177, L:K.177, L:K.177, L:R.295, L:R.295, L:R.295, L:G.329, L:G.329, L:G.380, L:I.382, L:I.382, L:Q.401, L:G.405 Salt bridges: L:K.175, L:K.175, L:K.177, L:R.295, L:H.327, L:K.334, L:K.334

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

EDO.3: 7 residues within 4Å: Chain A: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.3 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.20, E.52 Chain I: F.469 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: G.47, V.48, P.49, E.52 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: R.295, H.298, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: L.270 Chain I: L.270 Ligands: EDO.50 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain B: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: Y.20, E.52, A.129 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: R.295, H.298, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain C: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: Y.20, E.52 Chain K: F.469 Ligands: EDO.22 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain C: G.47, V.48, P.49, E.52 Ligands: EDO.21 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: L.270 Chain K: L.270 Ligands: EDO.66 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain D: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain D: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain D: Y.20, E.52 Chain J: F.469 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain D: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain D: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain D: L.270 Chain J: L.270 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: Y.226, K.227, A.230 Chain E: K.49, E.55, D.69 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain E: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain C: Y.226, K.227, A.230 Chain F: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain F: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain D: Y.226, K.227, A.230 Chain G: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain G: G.37, W.38, I.39, F.81, G.82, C.83, R.84 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain A: Y.226, K.227, A.230 Chain H: K.49, E.55, D.69 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain H: G.37, W.38, I.39, F.81, G.82, C.83, R.84 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain I: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.45 Ligand excluded by PLIP EDO.45: 9 residues within 4Å: Chain I: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.44 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain A: F.469 Chain I: Y.20, E.52 Ligands: EDO.47 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain I: G.47, V.48, P.49, E.52 Ligands: EDO.46 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain I: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain I: R.295, H.298, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.50: 3 residues within 4Å: Chain A: L.270 Chain I: L.270 Ligands: EDO.9 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain J: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.54 Ligand excluded by PLIP EDO.54: 9 residues within 4Å: Chain J: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.53 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain J: Y.20, E.52, A.129 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain J: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain J: R.295, H.298, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain K: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.61 Ligand excluded by PLIP EDO.61: 9 residues within 4Å: Chain K: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.60 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain C: F.469 Chain K: Y.20, E.52 Ligands: EDO.63 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain K: G.47, V.48, P.49, E.52 Ligands: EDO.62 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain K: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain K: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain C: L.270 Chain K: L.270 Ligands: EDO.25 Ligand excluded by PLIP EDO.69: 7 residues within 4Å: Chain L: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.70 Ligand excluded by PLIP EDO.70: 9 residues within 4Å: Chain L: G.16, V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.69 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain B: F.469 Chain L: Y.20, E.52 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain L: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.73: 7 residues within 4Å: Chain L: R.295, H.298, D.302, F.311, E.336, F.345, D.473 Ligand excluded by PLIP EDO.74: 2 residues within 4Å: Chain B: L.270 Chain L: L.270 Ligand excluded by PLIP EDO.75: 6 residues within 4Å: Chain J: Y.226, K.227, A.230 Chain M: K.49, E.55, D.69 Ligand excluded by PLIP EDO.76: 6 residues within 4Å: Chain M: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP EDO.77: 7 residues within 4Å: Chain K: Y.226, K.227, A.230 Chain N: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain N: G.37, W.38, I.39, F.81, G.82, C.83 Ligand excluded by PLIP EDO.79: 7 residues within 4Å: Chain L: Y.226, K.227, A.230 Chain O: K.49, E.55, S.56, D.69 Ligand excluded by PLIP EDO.80: 7 residues within 4Å: Chain O: G.37, W.38, I.39, F.81, G.82, C.83, R.84 Ligand excluded by PLIP EDO.81: 6 residues within 4Å: Chain I: Y.226, K.227, A.230 Chain P: K.49, E.55, D.69 Ligand excluded by PLIP EDO.82: 7 residues within 4Å: Chain P: G.37, W.38, I.39, F.81, G.82, C.83, R.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, T.C. et al., First Crystal Structure of Rubisco from a Green Alga, Chlamydomonas Reinhardtii. J.Biol.Chem. (2001)

Release Date

2001-10-24

Peptides

RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN: ABCDIJKL
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1: EFGHMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

I
A

J
C

K
E

L
G

E
I

F
K

G
M

H
O

M
I

N
K

O
M

P
O

RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAIN

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1

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