SMTL ID : 8bdb.2 (1 other biounit)

Ribulose-1,5-bisphosphate carboxylase/oxygenase from Griffithsia monilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: T.175, K.179, K.203, D.205, E.206 Chain M: N.125 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.205, A:E.206 MG.22: 8 residues within 4Å: Chain C: K.177, K.179, K.203, D.205, E.206, H.295 Chain O: N.125 Ligands: CAP.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.205, C:E.206 MG.48: 8 residues within 4Å: Chain E: T.175, K.179, K.203, D.205, E.206, H.295 Chain I: N.125 Ligands: CAP.49 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.205, E:E.206 MG.70: 8 residues within 4Å: Chain G: K.177, K.179, K.203, D.205, E.206, H.295 Chain K: N.125 Ligands: CAP.71 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.205, G:E.206 MG.91: 7 residues within 4Å: Chain E: N.125 Chain I: T.175, K.179, K.203, D.205, E.206 Ligands: CAP.92 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.205, I:E.206 MG.112: 8 residues within 4Å: Chain G: N.125 Chain K: K.177, K.179, K.203, D.205, E.206, H.295 Ligands: CAP.113 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.205, K:E.206 MG.138: 8 residues within 4Å: Chain A: N.125 Chain M: T.175, K.179, K.203, D.205, E.206, H.295 Ligands: CAP.139 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.205, M:E.206 MG.160: 8 residues within 4Å: Chain C: N.125 Chain O: K.177, K.179, K.203, D.205, E.206, H.295 Ligands: CAP.161 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.205, O:E.206

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

CAP.2: 22 residues within 4Å: Chain A: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, F.403, G.404, G.405 Chain M: E.62, T.67, W.68, N.125 Ligands: MG.1 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain M Hydrogen bonds: A:T.175, A:K.177, A:G.382, A:G.404, A:G.405, M:T.67, M:N.125 Water bridges: A:T.175, A:T.175, A:K.179, A:K.179, A:K.179, A:K.179, A:H.295, A:R.296, A:R.296, A:H.328, A:G.330, A:S.380, A:G.381, A:I.383, A:G.406 Salt bridges: A:K.177, A:K.177, A:K.179, A:R.296, A:H.328, A:K.335, A:K.335 CAP.23: 21 residues within 4Å: Chain C: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain O: E.62, T.67, W.68, N.125 Ligands: MG.22 31 PLIP interactions: 28 interactions with chain C, 3 interactions with chain O Hydrogen bonds: C:T.175, C:T.175, C:K.177, C:D.205, C:S.380, C:G.382, C:G.404, C:G.405, O:T.67, O:T.67, O:N.125 Water bridges: C:T.175, C:T.175, C:K.179, C:K.179, C:K.179, C:K.179, C:R.296, C:R.296, C:G.330, C:S.380, C:G.381, C:I.383, C:G.406 Salt bridges: C:K.177, C:K.177, C:K.179, C:R.296, C:H.328, C:K.335, C:K.335 CAP.49: 21 residues within 4Å: Chain E: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain I: E.62, T.67, W.68, N.125 Ligands: MG.48 32 PLIP interactions: 28 interactions with chain E, 4 interactions with chain I Hydrogen bonds: E:T.175, E:T.175, E:K.177, E:D.205, E:S.380, E:G.381, E:G.382, E:G.404, E:G.405, I:T.67, I:T.67, I:N.125 Water bridges: E:T.175, E:T.175, E:K.179, E:K.179, E:K.179, E:R.296, E:R.296, E:G.330, E:S.380, E:I.383, E:Q.402, E:G.406, I:E.62 Salt bridges: E:K.177, E:K.177, E:K.179, E:R.296, E:H.328, E:K.335, E:K.335 CAP.71: 21 residues within 4Å: Chain G: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain K: E.62, T.67, W.68, N.125 Ligands: MG.70 29 PLIP interactions: 26 interactions with chain G, 3 interactions with chain K Hydrogen bonds: G:T.175, G:T.175, G:K.177, G:G.382, G:G.404, G:G.405, K:T.67, K:T.67, K:N.125 Water bridges: G:T.175, G:T.175, G:K.179, G:K.179, G:K.179, G:K.179, G:R.296, G:R.296, G:G.330, G:S.380, G:G.381, G:I.383, G:G.406 Salt bridges: G:K.177, G:K.177, G:K.179, G:R.296, G:H.328, G:K.335, G:K.335 CAP.92: 22 residues within 4Å: Chain E: E.62, T.67, W.68, N.125 Chain I: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, F.403, G.404, G.405 Ligands: MG.91 30 PLIP interactions: 3 interactions with chain E, 27 interactions with chain I Hydrogen bonds: E:T.67, E:N.125, I:T.175, I:T.175, I:K.177, I:G.382, I:G.404, I:G.405 Water bridges: E:E.62, I:T.175, I:T.175, I:K.179, I:K.179, I:K.179, I:H.295, I:R.296, I:R.296, I:H.328, I:G.330, I:S.380, I:G.381, I:I.383, I:G.406 Salt bridges: I:K.177, I:K.177, I:K.179, I:R.296, I:H.328, I:K.335, I:K.335 CAP.113: 21 residues within 4Å: Chain G: E.62, T.67, W.68, N.125 Chain K: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.112 30 PLIP interactions: 27 interactions with chain K, 3 interactions with chain G Hydrogen bonds: K:T.175, K:K.177, K:D.205, K:S.380, K:G.382, K:G.404, K:G.405, G:T.67, G:T.67, G:N.125 Water bridges: K:T.175, K:T.175, K:K.179, K:K.179, K:K.179, K:K.179, K:R.296, K:R.296, K:G.330, K:S.380, K:G.381, K:I.383, K:G.406 Salt bridges: K:K.177, K:K.177, K:K.179, K:R.296, K:H.328, K:K.335, K:K.335 CAP.139: 21 residues within 4Å: Chain A: E.62, T.67, W.68, N.125 Chain M: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.138 31 PLIP interactions: 28 interactions with chain M, 3 interactions with chain A Hydrogen bonds: M:T.175, M:K.177, M:E.206, M:S.380, M:G.381, M:G.382, M:G.404, M:G.405, A:T.67, A:T.67, A:N.125 Water bridges: M:T.175, M:T.175, M:K.179, M:K.179, M:K.179, M:K.179, M:R.296, M:R.296, M:G.330, M:S.380, M:I.383, M:Q.402, M:G.406 Salt bridges: M:K.177, M:K.177, M:K.179, M:R.296, M:H.328, M:K.335, M:K.335 CAP.161: 21 residues within 4Å: Chain C: E.62, T.67, W.68, N.125 Chain O: T.175, K.177, K.179, K.203, D.205, E.206, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.160 28 PLIP interactions: 4 interactions with chain C, 24 interactions with chain O Hydrogen bonds: C:T.67, C:T.67, C:N.125, O:T.175, O:K.177, O:G.382, O:G.404, O:G.405 Water bridges: C:E.62, O:T.175, O:T.175, O:K.179, O:K.179, O:K.179, O:R.296, O:R.296, O:G.330, O:S.380, O:G.381, O:I.383, O:G.406 Salt bridges: O:K.177, O:K.177, O:K.179, O:R.296, O:H.328, O:K.335, O:K.335

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

EDO.3: 6 residues within 4Å: Chain A: K.287, N.288, D.289 Chain E: K.217, F.258 Chain F: S.118 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.217, F.258 Chain B: S.118 Chain G: N.288, D.289 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: P.212, F.213, M.214 Chain G: V.159, R.373 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.196, G.197, Q.415, T.419 Chain B: F.10 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: V.144, D.368, A.370, S.371 Chain B: R.89 Chain I: I.107, D.108 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.151, R.286 Chain E: R.215 Chain I: E.112 Ligands: BCT.105 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: L.352, L.355, E.356, N.358, Q.361 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: F.365, Q.366 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: V.159, R.163 Chain E: E.218, L.221, Y.222 Chain F: R.119 Ligands: EDO.21 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: A.232, A.233 Chain B: M.1, G.108, F.109 Chain H: E.134 Ligands: EDO.82 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: D.40, E.134, R.137 Chain F: F.109, R.110, L.111 Ligands: EDO.19, EDO.65 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: T.38, E.39, N.45, F.47, E.49, E.134 Chain E: R.229 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain B: E.115, R.119 Chain G: I.231, V.237, K.238, G.263, V.265 Chain H: R.44 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: R.44, N.46 Chain E: L.221, Y.222, E.225 Chain F: R.119, Q.121 Ligands: EDO.12 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: N.288, D.289 Chain G: K.217, F.258 Chain H: S.118 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain C: P.212, F.213, M.214 Chain E: V.159, R.373 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: E.90, F.100, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain C: I.9, Y.14, E.15, S.16, V.70, V.71, W.72 Chain O: I.408, G.409 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain C: D.368, A.370, S.371 Chain D: R.89 Chain K: I.107, D.108 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: Q.151, R.286 Chain G: R.215 Chain K: E.112 Ligands: BCT.127 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: R.196, G.197, Q.415, T.419 Chain D: F.10 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain C: V.159, R.163 Chain G: E.218, L.221, Y.222 Chain H: R.119 Ligands: EDO.45 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: L.352, L.355, E.356, N.358, Q.361 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: R.141, Q.366, Q.367, D.368 Ligands: EDO.34 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: R.141, F.365, Q.366 Ligands: EDO.33 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain C: A.232 Chain D: M.1, G.108, F.109 Chain F: E.134 Ligands: EDO.67 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain D: D.40, E.134, R.137 Chain H: F.109, R.110, L.111 Ligands: EDO.42, EDO.83 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain D: T.38, E.39, N.45, F.47, E.49, E.134 Chain G: R.229 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain D: D.16, G.69, R.72 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain D: V.112, R.113, S.114, K.122, Y.123, S.124 Chain H: S.114 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain D: R.44, N.46 Chain G: L.221, Y.222, E.225 Chain H: Q.121 Ligands: EDO.31 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain D: E.115, R.119 Chain E: I.231, V.237, K.238, G.263, V.265 Chain F: R.44 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain C: K.217, F.258 Chain D: I.117, S.118 Chain E: K.287, N.288, D.289 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain A: V.159, R.373 Chain E: P.212, F.213, M.214 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain C: E.218, L.221, Y.222 Chain D: R.119 Chain E: V.159, R.163 Ligands: EDO.69 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain E: R.436, D.437, Y.438, V.439 Ligand excluded by PLIP EDO.54: 8 residues within 4Å: Chain E: Y.14, S.16, V.70, V.71, W.72 Chain I: I.408, G.409, H.410 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain E: V.144, D.368, A.370, S.371 Chain F: R.89 Chain O: I.107, D.108 Ligand excluded by PLIP EDO.57: 8 residues within 4Å: Chain E: I.408, G.409, H.410 Chain I: Y.14, S.16, V.70, V.71, W.72 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain E: R.196, G.197, Q.415, T.419 Chain F: F.10 Ligand excluded by PLIP EDO.59: 2 residues within 4Å: Chain E: F.365, Q.366 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain E: P.443, R.447 Ligand excluded by PLIP EDO.64: 7 residues within 4Å: Chain A: I.231, V.237, K.238, G.263 Chain B: R.44 Chain F: E.115, R.119 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain B: E.134 Chain E: A.232, A.233 Chain F: M.1, G.108, F.109 Ligands: EDO.18 Ligand excluded by PLIP EDO.66: 8 residues within 4Å: Chain C: R.229 Chain F: T.38, E.39, N.45, F.47, E.49, E.134 Ligands: EDO.67 Ligand excluded by PLIP EDO.67: 8 residues within 4Å: Chain D: F.109, R.110, L.111 Chain F: D.40, E.134, R.137 Ligands: EDO.40, EDO.66 Ligand excluded by PLIP EDO.68: 7 residues within 4Å: Chain D: S.114 Chain F: V.112, R.113, S.114, K.122, Y.123, S.124 Ligand excluded by PLIP EDO.69: 8 residues within 4Å: Chain C: L.221, Y.222, E.225 Chain D: R.119, Q.121 Chain F: R.44, N.46 Ligands: EDO.52 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain C: V.159, R.373 Chain G: P.212, F.213, M.214 Ligand excluded by PLIP EDO.73: 7 residues within 4Å: Chain A: E.218, L.221, Y.222 Chain B: R.119 Chain G: V.159, R.163 Ligands: EDO.86 Ligand excluded by PLIP EDO.74: 8 residues within 4Å: Chain G: I.9, Y.14, S.16, V.70, V.71, W.72 Chain K: I.408, G.409 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain G: R.196, G.197, Q.415, T.419 Chain H: F.10 Ligand excluded by PLIP EDO.76: 8 residues within 4Å: Chain G: V.144, D.368, A.370, S.371 Chain H: R.89 Chain M: T.36, I.107, D.108 Ligand excluded by PLIP EDO.77: 4 residues within 4Å: Chain G: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.78: 2 residues within 4Å: Chain G: F.365, Q.366 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain G: L.351, L.352, K.374, D.398 Chain H: V.91 Ligand excluded by PLIP EDO.82: 8 residues within 4Å: Chain B: F.109, R.110, L.111 Chain H: D.40, E.134, R.137 Ligands: EDO.17, EDO.85 Ligand excluded by PLIP EDO.83: 7 residues within 4Å: Chain D: E.134 Chain G: A.232, A.233 Chain H: M.1, G.108, F.109 Ligands: EDO.41 Ligand excluded by PLIP EDO.84: 8 residues within 4Å: Chain C: I.231, V.237, K.238, G.263, V.265 Chain D: R.44 Chain H: E.115, R.119 Ligand excluded by PLIP EDO.85: 8 residues within 4Å: Chain A: R.229 Chain H: T.38, E.39, N.45, F.47, E.49, E.134 Ligands: EDO.82 Ligand excluded by PLIP EDO.86: 8 residues within 4Å: Chain A: L.221, Y.222, E.225 Chain B: R.119, Q.121 Chain H: R.44, N.46 Ligands: EDO.73 Ligand excluded by PLIP EDO.87: 8 residues within 4Å: Chain H: I.33, N.34, I.35, W.51, L.53, L.55, E.67 Chain M: T.7 Ligand excluded by PLIP EDO.88: 4 residues within 4Å: Chain H: D.13, I.100, N.101, R.102 Ligand excluded by PLIP EDO.89: 7 residues within 4Å: Chain B: S.114 Chain H: V.112, R.113, S.114, K.122, Y.123, S.124 Ligand excluded by PLIP EDO.93: 6 residues within 4Å: Chain I: K.287, N.288, D.289 Chain M: K.217, F.258 Chain N: S.118 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain I: K.217, F.258 Chain J: S.118 Chain O: N.288, D.289 Ligand excluded by PLIP EDO.95: 5 residues within 4Å: Chain I: P.212, F.213, M.214 Chain O: V.159, R.373 Ligand excluded by PLIP EDO.96: 4 residues within 4Å: Chain I: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.97: 5 residues within 4Å: Chain I: R.196, G.197, Q.415, T.419 Chain J: F.10 Ligand excluded by PLIP EDO.98: 7 residues within 4Å: Chain A: I.107, D.108 Chain I: V.144, D.368, A.370, S.371 Chain J: R.89 Ligand excluded by PLIP EDO.99: 5 residues within 4Å: Chain A: E.112 Chain I: Q.151, R.286 Chain M: R.215 Ligands: BCT.15 Ligand excluded by PLIP EDO.100: 5 residues within 4Å: Chain I: L.352, L.355, E.356, N.358, Q.361 Ligand excluded by PLIP EDO.101: 2 residues within 4Å: Chain I: F.365, Q.366 Ligand excluded by PLIP EDO.102: 7 residues within 4Å: Chain I: V.159, R.163 Chain M: E.218, L.221, Y.222 Chain N: R.119 Ligands: EDO.111 Ligand excluded by PLIP EDO.107: 7 residues within 4Å: Chain I: A.232, A.233 Chain J: M.1, G.108, F.109 Chain P: E.134 Ligands: EDO.172 Ligand excluded by PLIP EDO.108: 8 residues within 4Å: Chain J: D.40, E.134, R.137 Chain N: F.109, R.110, L.111 Ligands: EDO.109, EDO.155 Ligand excluded by PLIP EDO.109: 8 residues within 4Å: Chain J: T.38, E.39, N.45, F.47, E.49, E.134 Chain M: R.229 Ligands: EDO.108 Ligand excluded by PLIP EDO.110: 8 residues within 4Å: Chain J: E.115, R.119 Chain O: I.231, V.237, K.238, G.263, V.265 Chain P: R.44 Ligand excluded by PLIP EDO.111: 8 residues within 4Å: Chain J: R.44, N.46 Chain M: L.221, Y.222, E.225 Chain N: R.119, Q.121 Ligands: EDO.102 Ligand excluded by PLIP EDO.114: 5 residues within 4Å: Chain K: N.288, D.289 Chain O: K.217, F.258 Chain P: S.118 Ligand excluded by PLIP EDO.115: 5 residues within 4Å: Chain K: P.212, F.213, M.214 Chain M: V.159, R.373 Ligand excluded by PLIP EDO.116: 5 residues within 4Å: Chain K: E.90, F.100, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.117: 9 residues within 4Å: Chain G: I.408, G.409 Chain K: I.9, Y.14, E.15, S.16, V.70, V.71, W.72 Ligand excluded by PLIP EDO.118: 6 residues within 4Å: Chain C: I.107, D.108 Chain K: D.368, A.370, S.371 Chain L: R.89 Ligand excluded by PLIP EDO.119: 5 residues within 4Å: Chain C: E.112 Chain K: Q.151, R.286 Chain O: R.215 Ligands: BCT.37 Ligand excluded by PLIP EDO.120: 5 residues within 4Å: Chain K: R.196, G.197, Q.415, T.419 Chain L: F.10 Ligand excluded by PLIP EDO.121: 7 residues within 4Å: Chain K: V.159, R.163 Chain O: E.218, L.221, Y.222 Chain P: R.119 Ligands: EDO.135 Ligand excluded by PLIP EDO.122: 5 residues within 4Å: Chain K: L.352, L.355, E.356, N.358, Q.361 Ligand excluded by PLIP EDO.123: 5 residues within 4Å: Chain K: R.141, Q.366, Q.367, D.368 Ligands: EDO.124 Ligand excluded by PLIP EDO.124: 4 residues within 4Å: Chain K: R.141, F.365, Q.366 Ligands: EDO.123 Ligand excluded by PLIP EDO.130: 6 residues within 4Å: Chain K: A.232 Chain L: M.1, G.108, F.109 Chain N: E.134 Ligands: EDO.157 Ligand excluded by PLIP EDO.131: 8 residues within 4Å: Chain L: D.40, E.134, R.137 Chain P: F.109, R.110, L.111 Ligands: EDO.132, EDO.173 Ligand excluded by PLIP EDO.132: 8 residues within 4Å: Chain L: T.38, E.39, N.45, F.47, E.49, E.134 Chain O: R.229 Ligands: EDO.131 Ligand excluded by PLIP EDO.133: 3 residues within 4Å: Chain L: D.16, G.69, R.72 Ligand excluded by PLIP EDO.134: 7 residues within 4Å: Chain L: V.112, R.113, S.114, K.122, Y.123, S.124 Chain P: S.114 Ligand excluded by PLIP EDO.135: 7 residues within 4Å: Chain L: R.44, N.46 Chain O: L.221, Y.222, E.225 Chain P: Q.121 Ligands: EDO.121 Ligand excluded by PLIP EDO.136: 8 residues within 4Å: Chain L: E.115, R.119 Chain M: I.231, V.237, K.238, G.263, V.265 Chain N: R.44 Ligand excluded by PLIP EDO.140: 7 residues within 4Å: Chain K: K.217, F.258 Chain L: I.117, S.118 Chain M: K.287, N.288, D.289 Ligand excluded by PLIP EDO.141: 5 residues within 4Å: Chain I: V.159, R.373 Chain M: P.212, F.213, M.214 Ligand excluded by PLIP EDO.142: 7 residues within 4Å: Chain K: E.218, L.221, Y.222 Chain L: R.119 Chain M: V.159, R.163 Ligands: EDO.159 Ligand excluded by PLIP EDO.143: 4 residues within 4Å: Chain M: R.436, D.437, Y.438, V.439 Ligand excluded by PLIP EDO.144: 8 residues within 4Å: Chain A: I.408, G.409, H.410 Chain M: Y.14, S.16, V.70, V.71, W.72 Ligand excluded by PLIP EDO.145: 4 residues within 4Å: Chain M: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.146: 7 residues within 4Å: Chain G: I.107, D.108 Chain M: V.144, D.368, A.370, S.371 Chain N: R.89 Ligand excluded by PLIP EDO.147: 8 residues within 4Å: Chain A: Y.14, S.16, V.70, V.71, W.72 Chain M: I.408, G.409, H.410 Ligand excluded by PLIP EDO.148: 5 residues within 4Å: Chain M: R.196, G.197, Q.415, T.419 Chain N: F.10 Ligand excluded by PLIP EDO.149: 2 residues within 4Å: Chain M: F.365, Q.366 Ligand excluded by PLIP EDO.150: 2 residues within 4Å: Chain M: P.443, R.447 Ligand excluded by PLIP EDO.154: 7 residues within 4Å: Chain I: I.231, V.237, K.238, G.263 Chain J: R.44 Chain N: E.115, R.119 Ligand excluded by PLIP EDO.155: 7 residues within 4Å: Chain J: E.134 Chain M: A.232, A.233 Chain N: M.1, G.108, F.109 Ligands: EDO.108 Ligand excluded by PLIP EDO.156: 8 residues within 4Å: Chain K: R.229 Chain N: T.38, E.39, N.45, F.47, E.49, E.134 Ligands: EDO.157 Ligand excluded by PLIP EDO.157: 8 residues within 4Å: Chain L: F.109, R.110, L.111 Chain N: D.40, E.134, R.137 Ligands: EDO.130, EDO.156 Ligand excluded by PLIP EDO.158: 7 residues within 4Å: Chain L: S.114 Chain N: V.112, R.113, S.114, K.122, Y.123, S.124 Ligand excluded by PLIP EDO.159: 8 residues within 4Å: Chain K: L.221, Y.222, E.225 Chain L: R.119, Q.121 Chain N: R.44, N.46 Ligands: EDO.142 Ligand excluded by PLIP EDO.162: 5 residues within 4Å: Chain K: V.159, R.373 Chain O: P.212, F.213, M.214 Ligand excluded by PLIP EDO.163: 7 residues within 4Å: Chain I: E.218, L.221, Y.222 Chain J: R.119 Chain O: V.159, R.163 Ligands: EDO.176 Ligand excluded by PLIP EDO.164: 8 residues within 4Å: Chain C: I.408, G.409 Chain O: I.9, Y.14, S.16, V.70, V.71, W.72 Ligand excluded by PLIP EDO.165: 5 residues within 4Å: Chain O: R.196, G.197, Q.415, T.419 Chain P: F.10 Ligand excluded by PLIP EDO.166: 8 residues within 4Å: Chain E: T.36, I.107, D.108 Chain O: V.144, D.368, A.370, S.371 Chain P: R.89 Ligand excluded by PLIP EDO.167: 4 residues within 4Å: Chain O: E.90, Y.102, L.359, F.478 Ligand excluded by PLIP EDO.168: 2 residues within 4Å: Chain O: F.365, Q.366 Ligand excluded by PLIP EDO.169: 5 residues within 4Å: Chain O: L.351, L.352, K.374, D.398 Chain P: V.91 Ligand excluded by PLIP EDO.172: 8 residues within 4Å: Chain J: F.109, R.110, L.111 Chain P: D.40, E.134, R.137 Ligands: EDO.107, EDO.175 Ligand excluded by PLIP EDO.173: 7 residues within 4Å: Chain L: E.134 Chain O: A.232, A.233 Chain P: M.1, G.108, F.109 Ligands: EDO.131 Ligand excluded by PLIP EDO.174: 8 residues within 4Å: Chain K: I.231, V.237, K.238, G.263, V.265 Chain L: R.44 Chain P: E.115, R.119 Ligand excluded by PLIP EDO.175: 8 residues within 4Å: Chain I: R.229 Chain P: T.38, E.39, N.45, F.47, E.49, E.134 Ligands: EDO.172 Ligand excluded by PLIP EDO.176: 8 residues within 4Å: Chain I: L.221, Y.222, E.225 Chain J: R.119, Q.121 Chain P: R.44, N.46 Ligands: EDO.163 Ligand excluded by PLIP EDO.177: 8 residues within 4Å: Chain E: T.7 Chain P: I.33, N.34, I.35, W.51, L.53, L.55, E.67 Ligand excluded by PLIP EDO.178: 4 residues within 4Å: Chain P: D.13, I.100, N.101, R.102 Ligand excluded by PLIP EDO.179: 7 residues within 4Å: Chain J: S.114 Chain P: V.112, R.113, S.114, K.122, Y.123, S.124 Ligand excluded by PLIP

32 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.13: 3 residues within 4Å: Chain A: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.344 Water bridges: A:N.348 BCT.14: 4 residues within 4Å: Chain A: I.157, R.161, D.398 Chain B: V.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161 BCT.15: 5 residues within 4Å: Chain A: E.111, E.112 Chain M: E.251, R.255 Ligands: EDO.99 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain M Water bridges: A:E.112, M:R.215 BCT.16: 4 residues within 4Å: Chain A: D.393, D.437, Y.438, V.439 No protein-ligand interaction detected (PLIP) BCT.35: 3 residues within 4Å: Chain C: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.361, C:Q.361 BCT.36: 1 residues within 4Å: Chain C: G.49 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.49 BCT.37: 6 residues within 4Å: Chain C: E.111, E.112 Chain O: R.215, E.251, R.255 Ligands: EDO.119 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain C Hydrogen bonds: O:E.251, O:R.255, C:E.111 Water bridges: O:R.215, O:E.251 BCT.38: 2 residues within 4Å: Chain C: P.443, R.447 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.447, C:R.447 BCT.39: 3 residues within 4Å: Chain C: Q.444, R.447, K.451 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.451 BCT.47: 2 residues within 4Å: Chain D: D.13, L.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.13 BCT.61: 4 residues within 4Å: Chain E: T.467, F.468, N.469, Y.470 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.467, E:N.469, E:N.469 BCT.62: 3 residues within 4Å: Chain E: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.348, E:Q.361 BCT.63: 6 residues within 4Å: Chain B: E.49, E.134 Chain E: Y.192, R.196, R.229, A.233 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:E.134, E:R.196 BCT.80: 3 residues within 4Å: Chain G: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain G Water bridges: G:N.348, G:N.348 BCT.81: 2 residues within 4Å: Chain G: P.443, R.447 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.447, G:R.447 BCT.90: 6 residues within 4Å: Chain H: R.72, Q.73, Q.74, H.75, S.76, N.77 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.74 BCT.103: 3 residues within 4Å: Chain I: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.344 Water bridges: I:N.348 BCT.104: 4 residues within 4Å: Chain I: I.157, R.161, D.398 Chain J: V.91 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.161 BCT.105: 5 residues within 4Å: Chain E: E.251, R.255 Chain I: E.111, E.112 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain I Water bridges: E:R.215, E:E.251, I:E.112 BCT.106: 4 residues within 4Å: Chain I: D.393, D.437, Y.438, V.439 No protein-ligand interaction detected (PLIP) BCT.125: 3 residues within 4Å: Chain K: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.361, K:Q.361 BCT.126: 1 residues within 4Å: Chain K: G.49 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:G.49 BCT.127: 6 residues within 4Å: Chain G: R.215, E.251, R.255 Chain K: E.111, E.112 Ligands: EDO.29 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.251, G:R.255 Water bridges: G:R.215 BCT.128: 2 residues within 4Å: Chain K: P.443, R.447 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.447, K:R.447 BCT.129: 3 residues within 4Å: Chain K: Q.444, R.447, K.451 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:K.451 BCT.137: 2 residues within 4Å: Chain L: D.13, L.14 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.13 BCT.151: 4 residues within 4Å: Chain M: T.467, F.468, N.469, Y.470 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:T.467, M:T.467, M:N.469, M:N.469 BCT.152: 3 residues within 4Å: Chain M: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.348, M:Q.361 BCT.153: 6 residues within 4Å: Chain J: E.49, E.134 Chain M: Y.192, R.196, R.229, A.233 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain M Hydrogen bonds: J:E.134, M:R.196 Water bridges: J:E.134 BCT.170: 3 residues within 4Å: Chain O: R.344, N.348, Q.361 2 PLIP interactions: 2 interactions with chain O Water bridges: O:N.348, O:N.348 BCT.171: 2 residues within 4Å: Chain O: P.443, R.447 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:R.447, O:R.447 BCT.180: 6 residues within 4Å: Chain P: R.72, Q.73, Q.74, H.75, S.76, N.77 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth. Nat.Plants (2023)

Release Date

2023-06-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

E
I

G
K

I
E

K
G

M
I

O
K

B
F

D
H

F
J

H
L

J
F

L
H

N
J

P
L

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain

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