- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-8-8-mer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 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:4 interactions with chain M, 24 interactions with chain F- Hydrogen bonds: M:T.65, M:T.65, M:N.123, F:T.173, F:K.175, F:S.379, F:G.381, F:G.403, F:G.404
- Water bridges: M:E.60, 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
- 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
28 PLIP interactions:25 interactions with chain K, 3 interactions with chain O- Hydrogen bonds: K:T.173, 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:3 interactions with chain F, 26 interactions with chain M- Hydrogen bonds: F:T.65, F:T.65, F:N.123, 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
- 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 PLIPEDO.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 PLIPEDO.5: 4 residues within 4Å:- Chain A: Y.20, E.52, A.129
- Chain B: F.469
Ligand excluded by PLIPEDO.6: 4 residues within 4Å:- Chain A: K.466, F.467, E.468, F.469
Ligand excluded by PLIPEDO.7: 6 residues within 4Å:- Chain A: R.295, D.302, F.311, E.336, G.337, D.473
Ligand excluded by PLIPEDO.8: 4 residues within 4Å:- Chain A: L.270, G.273, M.297
- Chain B: L.270
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.13: 3 residues within 4Å:- Chain B: Y.20, E.52, A.129
Ligand excluded by PLIPEDO.14: 4 residues within 4Å:- Chain B: K.466, F.467, E.468, F.469
Ligand excluded by PLIPEDO.15: 7 residues within 4Å:- Chain B: R.295, H.298, S.328, G.329, E.336, G.337, D.473
Ligand excluded by PLIPEDO.16: 5 residues within 4Å:- Chain C: H.48, Y.52, E.54, H.55
- Chain O: A.230
Ligand excluded by PLIPEDO.17: 6 residues within 4Å:- Chain C: G.37, W.38, I.39, F.75, G.76, C.77
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.22: 3 residues within 4Å:- Chain D: Y.20, E.52, A.129
Ligand excluded by PLIPEDO.23: 5 residues within 4Å:- Chain D: K.466, F.467, E.468, F.469
- Ligands: EDO.38
Ligand excluded by PLIPEDO.24: 5 residues within 4Å:- Chain D: L.270, G.273, F.274
- Chain I: L.270, T.271
Ligand excluded by PLIPEDO.25: 5 residues within 4Å:- Chain E: G.37, W.38, I.39, F.75, G.76
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.30: 3 residues within 4Å:- Chain F: Y.20, E.52, A.129
Ligand excluded by PLIPEDO.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 PLIPEDO.32: 6 residues within 4Å:- Chain G: G.37, W.38, I.39, F.75, G.76, C.77
Ligand excluded by PLIPEDO.33: 5 residues within 4Å:- Chain H: G.37, W.38, I.39, F.75, G.76
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.38: 3 residues within 4Å:- Chain D: F.467
- Chain I: E.52
- Ligands: EDO.23
Ligand excluded by PLIPEDO.39: 4 residues within 4Å:- Chain I: K.466, F.467, E.468, F.469
Ligand excluded by PLIPEDO.40: 6 residues within 4Å:- Chain I: R.295, D.302, E.336, G.337, F.345, D.473
Ligand excluded by PLIPEDO.41: 6 residues within 4Å:- Chain J: G.37, W.38, I.39, F.75, G.76, C.77
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.46: 3 residues within 4Å:- Chain K: E.52
- Chain O: F.469
- Ligands: EDO.68
Ligand excluded by PLIPEDO.47: 5 residues within 4Å:- Chain K: K.466, F.467, E.468, F.469
- Ligands: EDO.67
Ligand excluded by PLIPEDO.48: 5 residues within 4Å:- Chain K: R.295, H.298, E.336, F.345, D.473
Ligand excluded by PLIPEDO.49: 6 residues within 4Å:- Chain J: Y.52, H.55, D.63
- Chain K: E.223, Y.226, K.227
Ligand excluded by PLIPEDO.50: 6 residues within 4Å:- Chain L: G.37, W.38, I.39, F.75, G.76, C.77
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.55: 5 residues within 4Å:- Chain F: F.469
- Chain M: Y.20, E.52, A.129
- Ligands: EDO.59
Ligand excluded by PLIPEDO.56: 4 residues within 4Å:- Chain M: K.466, F.467, E.468, F.469
Ligand excluded by PLIPEDO.57: 6 residues within 4Å:- Chain L: Y.52, H.55, D.63
- Chain M: E.223, Y.226, K.227
Ligand excluded by PLIPEDO.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 PLIPEDO.59: 3 residues within 4Å:- Chain F: K.466, F.467
- Ligands: EDO.55
Ligand excluded by PLIPEDO.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 PLIPEDO.61: 7 residues within 4Å:- Chain N: G.37, W.38, I.39, M.74, F.75, G.76, C.77
Ligand excluded by PLIPEDO.64: 4 residues within 4Å:- Chain K: L.270
- Chain O: L.270, G.273, F.274
Ligand excluded by PLIPEDO.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 PLIPEDO.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 PLIPEDO.67: 4 residues within 4Å:- Chain K: F.469
- Chain O: E.52, A.129
- Ligands: EDO.47
Ligand excluded by PLIPEDO.68: 5 residues within 4Å:- Chain O: K.466, F.467, E.468, F.469
- Ligands: EDO.46
Ligand excluded by PLIPEDO.69: 7 residues within 4Å:- Chain O: R.295, H.298, S.328, E.336, G.337, F.345, D.473
Ligand excluded by PLIPEDO.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
AB
BD
EF
HI
KK
OM
RO
VC
CE
FG
IH
JJ
ML
PN
TP
W
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-8-8-mer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)
- 54 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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
AB
BD
EF
HI
KK
OM
RO
VC
CE
FG
IH
JJ
ML
PN
TP
W