SMTL ID : 1wdd.1

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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 C: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.10: 8 residues within 4Å: Chain A: N.123 Chain C: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.22: 9 residues within 4Å: Chain E: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain G: N.123 Ligands: CAP.23 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.31: 8 residues within 4Å: Chain E: N.123 Chain G: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.32 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.43: 9 residues within 4Å: Chain I: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain K: N.123 Ligands: CAP.44 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.52: 8 residues within 4Å: Chain I: N.123 Chain K: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.53 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.64: 9 residues within 4Å: Chain M: T.173, K.175, K.177, K.201, D.203, E.204, H.294 Chain O: N.123 Ligands: CAP.65 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.73: 8 residues within 4Å: Chain M: N.123 Chain O: K.175, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.74 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 C: E.60, T.65, W.66, N.123 Ligands: MG.1 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.173, A:K.175, A:G.381, A:G.403, A:G.404, C:T.65, C:N.123 Water bridges: A:T.173, A:K.177, A:K.177, A:K.177, A:K.177, A:R.295, A:R.295, A:H.327, A:H.327, A:G.329, A:S.379, A:S.379, A:G.380, 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.11: 21 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 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 Ligands: MG.10 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.173, C:T.173, C:K.175, C:G.381, C:G.403, C:G.404, A:N.123 Water bridges: C:T.173, C:K.177, C:K.177, C:K.177, C:H.294, C:R.295, C:R.295, C:H.327, C:G.329, C:S.379, C:S.379, C:G.380, C:I.382, C:I.382, C:G.405, A: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.23: 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 G: E.60, T.65, W.66, N.123 Ligands: MG.22 29 PLIP interactions: 27 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:T.173, E:K.175, E:G.381, E:G.403, E:G.404, G:T.65, G:N.123 Water bridges: E:T.173, E:K.177, E:K.177, E:K.177, E:K.177, E:R.295, E:R.295, E:H.327, E:H.327, E:G.329, 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.32: 21 residues within 4Å: Chain E: E.60, T.65, W.66, N.123 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, G.403, G.404 Ligands: MG.31 30 PLIP interactions: 28 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:T.173, G:T.173, G:K.175, G:G.381, G:G.403, G:G.404, E:N.123 Water bridges: G:T.173, G:K.177, G:K.177, G:K.177, G:H.294, G:R.295, G:R.295, G:H.327, G:G.329, G:S.379, G:S.379, G:G.380, G:I.382, G:I.382, G:G.405, E: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.44: 22 residues within 4Å: 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 Chain K: E.60, T.65, W.66, N.123 Ligands: MG.43 29 PLIP interactions: 2 interactions with chain K, 27 interactions with chain I Hydrogen bonds: K:T.65, K:N.123, I:T.173, I:K.175, I:G.381, I:G.403, I:G.404 Water bridges: I:T.173, I:K.177, I:K.177, I:K.177, I:K.177, I:R.295, I:R.295, I:H.327, I:H.327, I:G.329, I:S.379, I:S.379, I:G.380, 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.53: 21 residues within 4Å: Chain I: 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.52 30 PLIP interactions: 28 interactions with chain K, 2 interactions with chain I Hydrogen bonds: K:T.173, K:T.173, K:K.175, K:G.381, K:G.403, K:G.404, I:N.123 Water bridges: K:T.173, K:K.177, K:K.177, K:K.177, K:H.294, 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, K:G.405, I:T.65 Salt bridges: K:K.175, K:K.175, K:K.177, K:R.295, K:H.327, K:K.334, K:K.334 CAP.65: 22 residues within 4Å: 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 Chain O: E.60, T.65, W.66, N.123 Ligands: MG.64 29 PLIP interactions: 27 interactions with chain M, 2 interactions with chain O Hydrogen bonds: M:T.173, M:K.175, M:G.381, M:G.403, M:G.404, O:T.65, O:N.123 Water bridges: M:T.173, M:K.177, M:K.177, M:K.177, M:K.177, M:R.295, M:R.295, M:H.327, M:H.327, M:G.329, M:S.379, 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.74: 21 residues within 4Å: Chain M: 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, G.403, G.404 Ligands: MG.73 31 PLIP interactions: 29 interactions with chain O, 2 interactions with chain M Hydrogen bonds: O:T.173, O:T.173, O:K.175, O:D.203, O:G.381, O:G.403, O:G.404, M:N.123 Water bridges: O:T.173, O:K.177, O:K.177, O:K.177, O:H.294, O:R.295, O:R.295, O:H.327, O:G.329, O:S.379, O:S.379, O:G.380, O:I.382, O:I.382, O:G.405, M: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

68 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligands: GOL.6 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: Y.20, E.52, A.129 Chain C: F.467, F.469 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: K.18, T.23, T.68, D.72, L.77 Ligands: GOL.4, GOL.7 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: V.11, F.13, T.68, V.69, W.70, G.73 Chain P: F.74 Ligands: GOL.6 Ligand excluded by PLIP GOL.8: 10 residues within 4Å: Chain A: K.183, R.187 Chain I: N.163 Chain J: E.43, R.64, Y.65, W.66, R.99, I.101, Q.110 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: L.22, T.23, L.77, D.78, K.81 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain C: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: L.270, F.274, I.301 Chain C: L.270, M.297 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: F.467 Chain C: Y.20, E.52, A.129 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain C: Y.226, Q.229, A.230 Chain D: V.50, Y.51, R.52, R.56 Chain P: E.53, N.54 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain C: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: F.13, T.68, V.69, W.70, D.72, G.73 Chain J: F.74 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain C: R.295, H.298, F.311, A.328, G.329, E.336, G.337, F.345 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain C: I.155, Q.156, R.319, R.350, D.351, D.352, P.372, G.373 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain C: N.163 Chain D: E.43, R.64, Y.65, W.66, R.99, Q.110 Chain K: K.183, R.187 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain D: Q.2, V.3 Chain P: W.69, A.92 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain E: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.25: 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: GOL.27 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain E: Y.20, E.52, A.129 Chain G: F.467, F.469 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain E: K.18, T.23, T.68, D.72, L.77 Ligands: GOL.25, GOL.28 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain E: V.11, F.13, T.68, V.69, W.70, G.73 Chain L: F.74 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 10 residues within 4Å: Chain E: K.183, R.187 Chain M: N.163 Chain N: E.43, R.64, Y.65, W.66, R.99, I.101, Q.110 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain E: L.22, T.23, L.77, D.78, K.81 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain G: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain E: L.270, F.274, I.301 Chain G: L.270, M.297 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain E: F.467 Chain G: Y.20, E.52, A.129 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain G: Y.226, Q.229, A.230 Chain H: V.50, Y.51, R.52, R.56 Chain L: E.53, N.54 Ligand excluded by PLIP GOL.37: 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.38: 7 residues within 4Å: Chain G: F.13, T.68, V.69, W.70, D.72, G.73 Chain N: F.74 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain G: R.295, H.298, F.311, A.328, G.329, E.336, G.337, F.345 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain G: I.155, Q.156, R.319, R.350, D.351, D.352, P.372, G.373 Ligand excluded by PLIP GOL.41: 9 residues within 4Å: Chain G: N.163 Chain H: E.43, R.64, Y.65, W.66, R.99, Q.110 Chain O: K.183, R.187 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain H: Q.2, V.3 Chain L: W.69, A.92 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain I: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.46: 10 residues within 4Å: Chain I: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligands: GOL.48 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain I: Y.20, E.52, A.129 Chain K: F.467, F.469 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain I: K.18, T.23, T.68, D.72, L.77 Ligands: GOL.46, GOL.49 Ligand excluded by PLIP GOL.49: 8 residues within 4Å: Chain D: F.74 Chain I: V.11, F.13, T.68, V.69, W.70, G.73 Ligands: GOL.48 Ligand excluded by PLIP GOL.50: 10 residues within 4Å: Chain E: N.163 Chain F: E.43, R.64, Y.65, W.66, R.99, I.101, Q.110 Chain I: K.183, R.187 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain I: L.22, T.23, L.77, D.78, K.81 Ligand excluded by PLIP GOL.54: 5 residues within 4Å: Chain K: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.55: 5 residues within 4Å: Chain I: L.270, F.274, I.301 Chain K: L.270, M.297 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain I: F.467 Chain K: Y.20, E.52, A.129 Ligand excluded by PLIP GOL.57: 9 residues within 4Å: Chain D: E.53, N.54 Chain K: Y.226, Q.229, A.230 Chain L: V.50, Y.51, R.52, R.56 Ligand excluded by PLIP GOL.58: 9 residues within 4Å: Chain K: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain F: F.74 Chain K: F.13, T.68, V.69, W.70, D.72, G.73 Ligand excluded by PLIP GOL.60: 8 residues within 4Å: Chain K: R.295, H.298, F.311, A.328, G.329, E.336, G.337, F.345 Ligand excluded by PLIP GOL.61: 8 residues within 4Å: Chain K: I.155, Q.156, R.319, R.350, D.351, D.352, P.372, G.373 Ligand excluded by PLIP GOL.62: 9 residues within 4Å: Chain G: K.183, R.187 Chain K: N.163 Chain L: E.43, R.64, Y.65, W.66, R.99, Q.110 Ligand excluded by PLIP GOL.63: 4 residues within 4Å: Chain D: W.69, A.92 Chain L: Q.2, V.3 Ligand excluded by PLIP GOL.66: 5 residues within 4Å: Chain M: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.67: 10 residues within 4Å: Chain M: G.16, V.17, K.18, Y.20, Y.24, T.65, W.66, T.67, T.68 Ligands: GOL.69 Ligand excluded by PLIP GOL.68: 5 residues within 4Å: Chain M: Y.20, E.52, A.129 Chain O: F.467, F.469 Ligand excluded by PLIP GOL.69: 7 residues within 4Å: Chain M: K.18, T.23, T.68, D.72, L.77 Ligands: GOL.67, GOL.70 Ligand excluded by PLIP GOL.70: 8 residues within 4Å: Chain H: F.74 Chain M: V.11, F.13, T.68, V.69, W.70, G.73 Ligands: GOL.69 Ligand excluded by PLIP GOL.71: 10 residues within 4Å: Chain A: N.163 Chain B: E.43, R.64, Y.65, W.66, R.99, I.101, Q.110 Chain M: K.183, R.187 Ligand excluded by PLIP GOL.72: 5 residues within 4Å: Chain M: L.22, T.23, L.77, D.78, K.81 Ligand excluded by PLIP GOL.75: 5 residues within 4Å: Chain O: K.32, T.34, P.104, L.105, D.106 Ligand excluded by PLIP GOL.76: 5 residues within 4Å: Chain M: L.270, F.274, I.301 Chain O: L.270, M.297 Ligand excluded by PLIP GOL.77: 4 residues within 4Å: Chain M: F.467 Chain O: Y.20, E.52, A.129 Ligand excluded by PLIP GOL.78: 9 residues within 4Å: Chain H: E.53, N.54 Chain O: Y.226, Q.229, A.230 Chain P: V.50, Y.51, R.52, R.56 Ligand excluded by PLIP GOL.79: 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 GOL.80: 7 residues within 4Å: Chain B: F.74 Chain O: F.13, T.68, V.69, W.70, D.72, G.73 Ligand excluded by PLIP GOL.81: 8 residues within 4Å: Chain O: R.295, H.298, F.311, A.328, G.329, E.336, G.337, F.345 Ligand excluded by PLIP GOL.82: 8 residues within 4Å: Chain O: I.155, Q.156, R.319, R.350, D.351, D.352, P.372, G.373 Ligand excluded by PLIP GOL.83: 9 residues within 4Å: Chain C: K.183, R.187 Chain O: N.163 Chain P: E.43, R.64, Y.65, W.66, R.99, Q.110 Ligand excluded by PLIP GOL.84: 4 residues within 4Å: Chain H: W.69, A.92 Chain P: Q.2, V.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumura, H. et al., Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate. J.Mol.Biol. (2012)

Release Date

2004-11-13

Peptides

Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain C: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
E

E
A

G
E

I
A

K
E

M
A

O
E

B
S

D
W

F
S

H
W

J
S

L
W

N
S

P
W

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain C

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