SMTL ID : 3axk.1

Structure of rice Rubisco in complex with NADP(H)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-oligomer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.270, G.273, M.297, I.301 Chain C: L.270, I.301 Ligand excluded by PLIP GOL.2: 5 residues within 4Å: Chain A: H.86, E.88, Y.100, K.356, R.358 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: R.213 Chain C: E.110 Chain I: S.145, K.146, F.148, Q.149, M.371 Ligands: GOL.7 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain C: T.147 Chain I: K.146, T.147, Q.149 Ligands: GOL.6 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain E: L.270, G.273, M.297, I.301 Chain G: L.270, I.301 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain E: H.86, E.88, Y.100, K.356, R.358 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain E: R.213 Chain G: E.110 Chain M: S.145, K.146, F.148, Q.149, M.371 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain G: T.147 Chain M: K.146, T.147, Q.149 Ligands: GOL.14 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain I: L.270, G.273, M.297, I.301 Chain K: L.270, I.301 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain I: H.86, E.88, Y.100, K.356, R.358 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain E: S.145, K.146, F.148, Q.149, M.371 Chain I: R.213 Chain K: E.110 Ligands: GOL.23 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain E: K.146, T.147, Q.149 Chain K: T.147 Ligands: GOL.22 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain M: L.270, G.273, M.297, I.301 Chain O: L.270, I.301 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain M: H.86, E.88, Y.100, K.356, R.358 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain A: S.145, K.146, F.148, Q.149, M.371 Chain M: R.213 Chain O: E.110 Ligands: GOL.31 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain A: K.146, T.147, Q.149 Chain O: T.147 Ligands: GOL.30 Ligand excluded by PLIP

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.134, H2O.206, H2O.327 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.843, H2O.867, H2O.905 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.1259, H2O.1331, H2O.1452 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.1968, H2O.1992, H2O.2030 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.2384, H2O.2456, H2O.2577 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.3093, H2O.3117, H2O.3155 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.3509, H2O.3581, H2O.3702 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.4218, H2O.4242, H2O.4280

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 24 PLIP interactions: 18 interactions with chain A, 6 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: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 32 PLIP interactions: 23 interactions with chain C, 9 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: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 24 PLIP interactions: 18 interactions with chain E, 6 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: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 32 PLIP interactions: 23 interactions with chain G, 9 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: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 24 PLIP interactions: 6 interactions with chain K, 18 interactions with chain I Hydrogen bonds: K:E.60, K:E.60, K:E.60, K:N.123, I:H.294, I:G.380, I:G.381, I:I.382, I:G.403, I:G.404 Water bridges: K:G.126, K:K.128, I:T.173, I:H.298, I:H.298, I:H.327, I:G.329, I:S.379, I:I.382, I:G.405 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 32 PLIP interactions: 23 interactions with chain K, 9 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: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 24 PLIP interactions: 18 interactions with chain M, 6 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: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 32 PLIP interactions: 9 interactions with chain M, 23 interactions with chain O Hydrogen bonds: M:E.60, M:E.60, M:T.68, M:T.68, M:T.68, M:N.123, 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 Water bridges: M:N.123, M:G.126, M:K.128, 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 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
A

C
B

E
A

G
B

I
A

K
B

M
A

O
B

B
S

D
T

F
S

H
T

J
S

L
T

N
S

P
T

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain, chloroplastic

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