SMTL ID : 1rxo.1

ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-8-8-mer

Ligands

8 x RUB: RIBULOSE-1,5-DIPHOSPHATE(Non-covalent)

RUB.1: 17 residues within 4Å: Chain A: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Chain M: W.66 Ligands: CA.2 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain M Hydrogen bonds: A:K.175, A:G.329, A:S.379, A:G.380, A:G.381, A:G.403, A:G.404 Water bridges: A:K.177, A:R.295, A:H.298, A:I.382, A:I.382, A:I.382, A:Q.401, A:F.402, M:W.66 Salt bridges: A:K.175, A:R.295, A:H.298 RUB.3: 17 residues within 4Å: Chain C: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Chain K: W.66 Ligands: CA.4 19 PLIP interactions: 1 interactions with chain K, 18 interactions with chain C Water bridges: K:W.66, C:K.177, C:R.295, C:H.298, C:I.382, C:I.382, C:I.382, C:Q.401, C:F.402 Hydrogen bonds: C:K.175, C:G.329, C:S.379, C:G.380, C:G.381, C:G.403, C:G.404 Salt bridges: C:K.175, C:R.295, C:H.298 RUB.5: 17 residues within 4Å: Chain E: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Chain I: W.66 Ligands: CA.6 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain I Hydrogen bonds: E:K.175, E:G.329, E:S.379, E:G.380, E:G.381, E:G.403, E:G.404 Water bridges: E:K.177, E:R.295, E:H.298, E:I.382, E:I.382, E:I.382, E:Q.401, E:F.402, I:W.66 Salt bridges: E:K.175, E:R.295, E:H.298 RUB.7: 17 residues within 4Å: Chain G: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Chain O: W.66 Ligands: CA.8 19 PLIP interactions: 18 interactions with chain G, 1 interactions with chain O Hydrogen bonds: G:K.175, G:G.329, G:S.379, G:G.380, G:G.381, G:G.403, G:G.404 Water bridges: G:K.177, G:R.295, G:H.298, G:I.382, G:I.382, G:I.382, G:Q.401, G:F.402, O:W.66 Salt bridges: G:K.175, G:R.295, G:H.298 RUB.9: 17 residues within 4Å: Chain E: W.66 Chain I: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: CA.10 21 PLIP interactions: 19 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:K.175, I:D.203, I:G.329, I:S.379, I:G.380, I:G.381, I:G.403, I:G.404 Water bridges: I:K.177, I:R.295, I:H.298, I:I.382, I:I.382, I:I.382, I:Q.401, I:F.402, E:T.65, E:W.66 Salt bridges: I:K.175, I:R.295, I:H.298 RUB.11: 17 residues within 4Å: Chain C: W.66 Chain K: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: CA.12 21 PLIP interactions: 19 interactions with chain K, 2 interactions with chain C Hydrogen bonds: K:K.175, K:D.203, K:G.329, K:S.379, K:G.380, K:G.381, K:G.403, K:G.404 Water bridges: K:K.177, K:R.295, K:H.298, K:I.382, K:I.382, K:I.382, K:Q.401, K:F.402, C:T.65, C:W.66 Salt bridges: K:K.175, K:R.295, K:H.298 RUB.13: 17 residues within 4Å: Chain A: W.66 Chain M: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: CA.14 21 PLIP interactions: 19 interactions with chain M, 2 interactions with chain A Hydrogen bonds: M:K.175, M:D.203, M:G.329, M:S.379, M:G.380, M:G.381, M:G.403, M:G.404 Water bridges: M:K.177, M:R.295, M:H.298, M:I.382, M:I.382, M:I.382, M:Q.401, M:F.402, A:T.65, A:W.66 Salt bridges: M:K.175, M:R.295, M:H.298 RUB.15: 17 residues within 4Å: Chain G: W.66 Chain O: K.175, K.201, D.203, E.204, H.294, R.295, H.298, H.327, G.329, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: CA.16 21 PLIP interactions: 19 interactions with chain O, 2 interactions with chain G Hydrogen bonds: O:K.175, O:D.203, O:G.329, O:S.379, O:G.380, O:G.381, O:G.403, O:G.404 Water bridges: O:K.177, O:R.295, O:H.298, O:I.382, O:I.382, O:I.382, O:Q.401, O:F.402, G:T.65, G:W.66 Salt bridges: O:K.175, O:R.295, O:H.298

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: K.201, D.203, E.204 Ligands: RUB.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.203, A:E.204, H2O.5 CA.4: 4 residues within 4Å: Chain C: K.201, D.203, E.204 Ligands: RUB.3 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.203, C:E.204, H2O.14 CA.6: 4 residues within 4Å: Chain E: K.201, D.203, E.204 Ligands: RUB.5 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:E.204, H2O.24 CA.8: 4 residues within 4Å: Chain G: K.201, D.203, E.204 Ligands: RUB.7 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.203, G:E.204, H2O.34 CA.10: 4 residues within 4Å: Chain I: K.201, D.203, E.204 Ligands: RUB.9 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.203, I:E.204, H2O.44 CA.12: 4 residues within 4Å: Chain K: K.201, D.203, E.204 Ligands: RUB.11 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.203, K:E.204, H2O.54 CA.14: 4 residues within 4Å: Chain M: K.201, D.203, E.204 Ligands: RUB.13 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:D.203, M:E.204, H2O.64 CA.16: 4 residues within 4Å: Chain O: K.201, D.203, E.204 Ligands: RUB.15 3 PLIP interactions: 2 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:D.203, O:E.204, H2O.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, T.C. et al., The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. J.Mol.Biol. (1997)

Release Date

1997-06-16

Peptides

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE: ACEGIKMO
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
B

E
E

G
H

I
L

K
B

M
E

O
H

B
S

D
C

F
F

H
I

J
S

L
C

N
F

P
I

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

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