SMTL ID : 1uzd.1

Chlamydomonas,Spinach Chimeric Rubisco

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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 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 B: T.173, 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.18: 7 residues within 4Å: Chain D: K.175, K.177, K.201, D.203, E.204 Chain I: N.123 Ligands: CAP.19 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.203, D:E.204 MG.26: 8 residues within 4Å: Chain F: K.175, K.177, K.201, D.203, E.204, H.294 Chain M: N.123 Ligands: CAP.27 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.203, F:E.204 MG.34: 7 residues within 4Å: Chain D: N.123 Chain I: K.177, K.201, D.203, E.204, H.294 Ligands: CAP.35 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.42: 7 residues within 4Å: Chain K: K.175, K.177, K.201, D.203, E.204 Chain O: N.123 Ligands: CAP.43 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.51: 7 residues within 4Å: Chain F: N.123 Chain M: K.177, K.201, D.203, E.204, H.294 Ligands: CAP.52 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.62: 7 residues within 4Å: Chain K: N.123 Chain O: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.63 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: 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 B: E.60, T.65, W.66, N.123 Ligands: MG.1 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.173, A:T.173, A:K.175, A:S.379, A:G.380, A:G.381, A:G.403, A:G.404, 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:R.295, A:S.379, A:S.379, A:I.382, A:I.382, A:Q.401, 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.10: 22 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, F.402, G.403, G.404 Ligands: MG.9 30 PLIP interactions: 26 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.173, B:K.175, B:S.379, B:G.381, B:G.403, B:G.404, A:T.65, A:T.65, A:N.123 Water bridges: B:T.173, B:K.177, B:K.177, B:K.177, B:R.295, B:R.295, B:R.295, B:G.329, B:S.379, B:S.379, B:G.380, B:G.405, B:G.405, A:E.60 Salt bridges: B:K.175, B:K.175, B:K.177, B:R.295, B:H.327, B:K.334, B:K.334 CAP.19: 23 residues within 4Å: Chain D: 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.18 28 PLIP interactions: 24 interactions with chain D, 4 interactions with chain I Hydrogen bonds: D:T.173, D:K.175, D:H.298, D:S.379, D:G.381, D:G.403, D:G.404, I:T.65, I:T.65, I:N.123 Water bridges: D:T.173, D:T.173, D:K.177, D:K.177, D:K.177, D:R.295, D:R.295, D:S.379, D:I.382, D:G.405, I:E.60 Salt bridges: D:K.175, D:K.175, D:K.177, D:R.295, D:H.327, D:K.334, D:K.334 CAP.27: 22 residues within 4Å: 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 Chain M: E.60, T.65, W.66, N.123 Ligands: MG.26 28 PLIP interactions: 24 interactions with chain F, 4 interactions with chain M Hydrogen bonds: F:T.173, F:K.175, F:S.379, F:G.381, F:G.403, F:G.404, M:T.65, M:T.65, M:N.123 Water bridges: F:T.173, F:T.173, F:K.177, F:K.177, F:K.177, F:R.295, F:R.295, F:G.329, F:G.380, F:I.382, F:G.405, M:E.60 Salt bridges: F:K.175, F:K.175, F:K.177, F:R.295, F:H.327, F:K.334, F:K.334 CAP.35: 23 residues within 4Å: Chain D: 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.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.34 30 PLIP interactions: 27 interactions with chain I, 3 interactions with chain D Hydrogen bonds: I:T.173, I:T.173, I:K.175, I:H.298, I:S.379, I:S.379, I:G.381, I:G.403, I:G.404, D:T.65, D:N.123 Water bridges: I:T.173, I:T.173, I:K.177, I:R.295, I:R.295, I:R.295, I:S.328, I:G.329, I:G.380, I:G.405, I:G.405, D:T.65 Salt bridges: I:K.175, I:K.175, I:K.177, I:R.295, I:H.327, I:K.334, I:K.334 CAP.43: 22 residues within 4Å: 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 Chain O: E.60, T.65, W.66, N.123 Ligands: MG.42 27 PLIP interactions: 24 interactions with chain K, 3 interactions with chain O Hydrogen bonds: K:T.173, K:K.175, K:S.379, K:G.381, K:G.403, K:G.404, O:T.65, O:T.65, O:N.123 Water bridges: K:K.177, K:K.177, K:K.177, K:R.295, K:R.295, K:R.295, K:H.298, K:K.334, 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.52: 22 residues within 4Å: Chain F: 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, G.403, G.404 Ligands: MG.51 29 PLIP interactions: 26 interactions with chain M, 3 interactions with chain F Hydrogen bonds: M:T.173, M:T.173, M:K.175, M:H.298, M:S.379, M:G.380, M:G.381, M:G.403, M:G.404, F:T.65, F:T.65, F:N.123 Water bridges: M:K.177, M:K.177, M:R.295, M:R.295, M:R.295, M:G.329, M:G.329, M:S.379, M:I.382, M:Q.401 Salt bridges: M:K.175, M:K.175, M:K.177, M:R.295, M:H.327, M:K.334, M:K.334 CAP.63: 23 residues within 4Å: Chain K: 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.62 31 PLIP interactions: 27 interactions with chain O, 4 interactions with chain K Hydrogen bonds: O:T.173, O:K.175, O:D.203, O:H.298, O:S.379, O:G.381, O:G.403, O:G.404, K:T.65, K:T.65, K:N.123 Water bridges: O:T.173, O:K.177, O:K.177, O:K.177, O:R.295, O:R.295, O:A.296, O:G.329, O:S.379, O:G.380, O:G.405, O:G.405, K: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

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

EDO.3: 6 residues within 4Å: Chain A: Y.24, G.64, T.68, V.69, D.72 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, A.129 Chain B: F.469 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: R.295, D.302, F.311, E.336, G.337, D.473 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: L.270, G.273, M.297 Chain B: L.270 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: Y.24, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 10 residues within 4Å: Chain B: G.16, V.17, K.18, D.19, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: Y.20, E.52, A.129 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: 7 residues within 4Å: Chain B: R.295, H.298, S.328, G.329, E.336, G.337, D.473 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain C: H.48, Y.52, E.54, H.55 Chain O: A.230 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: G.37, W.38, I.39, F.75, G.76, C.77 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain D: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain D: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: Y.20, E.52, A.129 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain D: K.466, F.467, E.468, F.469 Ligands: EDO.38 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain D: L.270, G.273, F.274 Chain I: L.270, T.271 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain E: G.37, W.38, I.39, F.75, G.76 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain F: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain F: 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 F: Y.20, E.52, A.129 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain F: R.295, H.298, S.328, G.329, E.336, G.337, F.345, D.473 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain G: G.37, W.38, I.39, F.75, G.76, C.77 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain H: G.37, W.38, I.39, F.75, G.76 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain I: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.37 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain I: K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.36 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain D: F.467 Chain I: E.52 Ligands: EDO.23 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain I: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain I: R.295, D.302, E.336, G.337, F.345, D.473 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain J: G.37, W.38, I.39, F.75, G.76, C.77 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain K: Y.24, G.64, T.68, V.69, D.72, L.77 Ligands: EDO.45 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain K: V.17, K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.44 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain K: E.52 Chain O: F.469 Ligands: EDO.68 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain K: K.466, F.467, E.468, F.469 Ligands: EDO.67 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain K: R.295, H.298, E.336, F.345, D.473 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain J: Y.52, H.55, D.63 Chain K: E.223, Y.226, K.227 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain L: G.37, W.38, I.39, F.75, G.76, C.77 Ligand excluded by PLIP EDO.53: 8 residues within 4Å: Chain M: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.54 Ligand excluded by PLIP EDO.54: 8 residues within 4Å: Chain M: K.18, D.19, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.53 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain F: F.469 Chain M: Y.20, E.52, A.129 Ligands: EDO.59 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain M: K.466, F.467, E.468, F.469 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain L: Y.52, H.55, D.63 Chain M: E.223, Y.226, K.227 Ligand excluded by PLIP EDO.58: 7 residues within 4Å: Chain F: L.270, G.273, F.274 Chain M: L.270, T.271, G.272, G.273 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain F: K.466, F.467 Ligands: EDO.55 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain A: Y.226, K.227, A.230 Chain N: H.48, Y.52, E.54, H.55 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain N: G.37, W.38, I.39, M.74, F.75, G.76, C.77 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain K: L.270 Chain O: L.270, G.273, F.274 Ligand excluded by PLIP EDO.65: 8 residues within 4Å: Chain O: Y.24, G.64, T.67, T.68, V.69, D.72, L.77 Ligands: EDO.66 Ligand excluded by PLIP EDO.66: 7 residues within 4Å: Chain O: K.18, Y.20, T.65, W.66, T.67, T.68 Ligands: EDO.65 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain K: F.469 Chain O: E.52, A.129 Ligands: EDO.47 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain O: K.466, F.467, E.468, F.469 Ligands: EDO.46 Ligand excluded by PLIP EDO.69: 7 residues within 4Å: Chain O: R.295, H.298, S.328, E.336, G.337, F.345, D.473 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain P: G.37, W.38, I.39, G.76, C.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karkehabadi, S. et al., Chimeric Small Subunits Influence Catalysis without Causing Global Conformational Changes in the Crystal Structure of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase. Biochemistry (2005)

Release Date

2005-05-31

Peptides

Ribulose bisphosphate carboxylase large chain: ABDFIKMO
Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic: CEGHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
E

F
H

I
K

K
O

M
R

O
V

C
C

E
F

G
I

H
J

J
M

L
P

N
T

P
W

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain 1, chloroplastic,Ribulose bisphosphate carboxylase small chain 2, chloroplastic,Ribulose bisphosphate carboxylase small chain 1, chloroplastic

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