- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- hetero-8-8-mer
- Ligands
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 3 residues within 4Å:- Chain A: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.203, A:E.204, H2O.6, H2O.8, H2O.13
MG.8: 3 residues within 4Å:- Chain C: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:D.203, C:E.204, H2O.33, H2O.34, H2O.35
MG.11: 3 residues within 4Å:- Chain E: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:D.203, E:E.204, H2O.49, H2O.52, H2O.56
MG.16: 3 residues within 4Å:- Chain G: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain G, 3 Ligand-Water interactions- Metal complexes: G:D.203, G:E.204, H2O.76, H2O.77, H2O.79
MG.19: 3 residues within 4Å:- Chain I: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain I, 3 Ligand-Water interactions- Metal complexes: I:D.203, I:E.204, H2O.92, H2O.95, H2O.100
MG.24: 3 residues within 4Å:- Chain K: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain K, 3 Ligand-Water interactions- Metal complexes: K:D.203, K:E.204, H2O.119, H2O.120, H2O.122
MG.27: 3 residues within 4Å:- Chain M: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain M, 3 Ligand-Water interactions- Metal complexes: M:D.203, M:E.204, H2O.135, H2O.138, H2O.143
MG.32: 3 residues within 4Å:- Chain O: K.201, D.203, E.204
5 PLIP interactions:2 interactions with chain O, 3 Ligand-Water interactions- Metal complexes: O:D.203, O:E.204, H2O.163, H2O.164, H2O.165
- 8 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NDP.4: 16 residues within 4Å:- Chain A: K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
- Chain C: E.60, N.123, G.126, F.127
23 PLIP interactions:18 interactions with chain A, 5 interactions with chain C- Hydrogen bonds: A:H.294, A:G.380, A:G.381, A:I.382, A:G.403, A:G.404, C:E.60, C:E.60, C:N.123
- Water bridges: A:T.173, A:H.298, A:H.298, A:H.327, A:G.329, A:S.379, A:I.382, A:G.405, C:G.126, C:K.128
- Salt bridges: A:K.175, A:K.175, A:R.295, A:H.298
NDP.5: 18 residues within 4Å:- Chain A: E.60, T.68, N.123, G.126, F.127
- Chain C: T.173, K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
31 PLIP interactions:23 interactions with chain C, 8 interactions with chain A- Hydrogen bonds: C:T.173, C:H.294, C:S.379, C:G.380, C:G.381, C:G.381, C:I.382, C:I.382, C:G.403, C:G.404, A:E.60, A:T.68, A:T.68, A:T.68, A:N.123
- Water bridges: C:K.175, C:K.175, C:R.295, C:R.295, C:H.298, C:H.327, C:A.328, C:T.330, C:G.405, C:G.405, A:N.123, A:G.126, A:K.128
- Salt bridges: C:K.175, C:R.295, C:H.298
NDP.12: 16 residues within 4Å:- Chain E: K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
- Chain G: E.60, N.123, G.126, F.127
23 PLIP interactions:18 interactions with chain E, 5 interactions with chain G- Hydrogen bonds: E:H.294, E:G.380, E:G.381, E:I.382, E:G.403, E:G.404, G:E.60, G:E.60, G:N.123
- Water bridges: E:T.173, E:H.298, E:H.298, E:H.327, E:G.329, E:S.379, E:I.382, E:G.405, G:G.126, G:K.128
- Salt bridges: E:K.175, E:K.175, E:R.295, E:H.298
NDP.13: 18 residues within 4Å:- Chain E: E.60, T.68, N.123, G.126, F.127
- Chain G: T.173, K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
31 PLIP interactions:23 interactions with chain G, 8 interactions with chain E- Hydrogen bonds: G:T.173, G:H.294, G:S.379, G:G.380, G:G.381, G:G.381, G:I.382, G:I.382, G:G.403, G:G.404, E:E.60, E:T.68, E:T.68, E:T.68, E:N.123
- Water bridges: G:K.175, G:K.175, G:R.295, G:R.295, G:H.298, G:H.327, G:A.328, G:T.330, G:G.405, G:G.405, E:N.123, E:G.126, E:K.128
- Salt bridges: G:K.175, G:R.295, G:H.298
NDP.20: 16 residues within 4Å:- Chain I: K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
- Chain K: E.60, N.123, G.126, F.127
23 PLIP interactions:18 interactions with chain I, 5 interactions with chain K- Hydrogen bonds: I:H.294, I:G.380, I:G.381, I:I.382, I:G.403, I:G.404, K:E.60, K:E.60, K:N.123
- Water bridges: I:T.173, I:H.298, I:H.298, I:H.327, I:G.329, I:S.379, I:I.382, I:G.405, K:G.126, K:K.128
- Salt bridges: I:K.175, I:K.175, I:R.295, I:H.298
NDP.21: 18 residues within 4Å:- Chain I: E.60, T.68, N.123, G.126, F.127
- Chain K: T.173, K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
31 PLIP interactions:23 interactions with chain K, 8 interactions with chain I- Hydrogen bonds: K:T.173, K:H.294, K:S.379, K:G.380, K:G.381, K:G.381, K:I.382, K:I.382, K:G.403, K:G.404, I:E.60, I:T.68, I:T.68, I:T.68, I:N.123
- Water bridges: K:K.175, K:K.175, K:R.295, K:R.295, K:H.298, K:H.327, K:A.328, K:T.330, K:G.405, K:G.405, I:N.123, I:G.126, I:K.128
- Salt bridges: K:K.175, K:R.295, K:H.298
NDP.28: 16 residues within 4Å:- Chain M: K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
- Chain O: E.60, N.123, G.126, F.127
23 PLIP interactions:18 interactions with chain M, 5 interactions with chain O- Hydrogen bonds: M:H.294, M:G.380, M:G.381, M:I.382, M:G.403, M:G.404, O:E.60, O:E.60, O:N.123
- Water bridges: M:T.173, M:H.298, M:H.298, M:H.327, M:G.329, M:S.379, M:I.382, M:G.405, O:G.126, O:K.128
- Salt bridges: M:K.175, M:K.175, M:R.295, M:H.298
NDP.29: 18 residues within 4Å:- Chain M: E.60, T.68, N.123, G.126, F.127
- Chain O: T.173, K.175, H.294, R.295, H.298, G.329, S.379, G.380, G.381, I.382, G.403, G.404, G.405
31 PLIP interactions:23 interactions with chain O, 8 interactions with chain M- Hydrogen bonds: O:T.173, O:H.294, O:S.379, O:G.380, O:G.381, O:G.381, O:I.382, O:I.382, O:G.403, O:G.404, M:E.60, M:T.68, M:T.68, M:T.68, M:N.123
- Water bridges: O:K.175, O:K.175, O:R.295, O:R.295, O:H.298, O:H.327, O:A.328, O:T.330, O:G.405, O:G.405, M:N.123, M:G.126, M:K.128
- Salt bridges: O:K.175, O:R.295, O:H.298
- 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
- 2012-04-11
- Peptides
- Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain, chloroplastic: BDFHJLNP - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
BE
AG
BI
AK
BM
AO
BB
SD
TF
SH
TJ
SL
TN
SP
T
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- hetero-8-8-mer
- Ligands
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 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
- 2012-04-11
- Peptides
- Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain, chloroplastic: BDFHJLNP - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
BE
AG
BI
AK
BM
AO
BB
SD
TF
SH
TJ
SL
TN
SP
T