SMTL ID : 1bwv.1

Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: T.182, K.210, D.212, E.213 Chain K: N.132 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.212, A:E.213 MG.3: 6 residues within 4Å: Chain C: T.182, K.210, D.212, E.213 Chain I: N.132 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.212, C:E.213 MG.5: 6 residues within 4Å: Chain E: T.182, K.210, D.212, E.213 Chain O: N.132 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.212, E:E.213 MG.7: 6 residues within 4Å: Chain G: T.182, K.210, D.212, E.213 Chain M: N.132 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.212, G:E.213 MG.9: 6 residues within 4Å: Chain C: N.132 Chain I: T.182, K.210, D.212, E.213 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.212, I:E.213 MG.11: 6 residues within 4Å: Chain A: N.132 Chain K: T.182, K.210, D.212, E.213 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.212, K:E.213 MG.13: 6 residues within 4Å: Chain G: N.132 Chain M: T.182, K.210, D.212, E.213 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.212, M:E.213 MG.15: 6 residues within 4Å: Chain E: N.132 Chain O: T.182, K.210, D.212, E.213 Ligands: CAP.16 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.212, O:E.213

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

CAP.2: 22 residues within 4Å: Chain A: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Chain K: E.69, T.74, W.75, N.132 Ligands: MG.1 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain K Hydrogen bonds: A:K.184, A:D.212, A:S.387, A:G.388, A:G.389, A:G.411, A:G.412, K:T.74, K:N.132 Water bridges: A:T.182, A:T.182, A:K.186, A:K.186, A:H.335, A:G.337, A:K.342, A:K.342, A:I.390, A:I.390, A:I.390 Salt bridges: A:K.184, A:K.184, A:K.186, A:R.303, A:H.335, A:K.342, A:K.342 CAP.4: 22 residues within 4Å: Chain C: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Chain I: E.69, T.74, W.75, N.132 Ligands: MG.3 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:T.182, C:K.184, C:D.212, C:G.388, C:G.389, C:G.411, C:G.412, I:T.74, I:N.132 Water bridges: C:T.182, C:T.182, C:K.186, C:K.186, C:G.337, C:K.342, C:K.342, C:S.387, C:G.388, C:I.390, C:I.390, C:I.390 Salt bridges: C:K.184, C:K.184, C:K.186, C:R.303, C:H.335, C:K.342, C:K.342 CAP.6: 22 residues within 4Å: Chain E: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Chain O: E.69, T.74, W.75, N.132 Ligands: MG.5 26 PLIP interactions: 22 interactions with chain E, 4 interactions with chain O Hydrogen bonds: E:T.182, E:K.184, E:D.212, E:G.388, E:G.389, E:G.411, E:G.412, O:T.74, O:N.132 Water bridges: E:T.182, E:T.182, E:K.342, E:K.342, E:S.387, E:I.390, E:I.390, E:I.390, O:E.69, O:E.69 Salt bridges: E:K.184, E:K.184, E:K.186, E:R.303, E:H.335, E:K.342, E:K.342 CAP.8: 22 residues within 4Å: Chain G: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Chain M: E.69, T.74, W.75, N.132 Ligands: MG.7 26 PLIP interactions: 23 interactions with chain G, 3 interactions with chain M Hydrogen bonds: G:K.184, G:D.212, G:S.387, G:G.388, G:G.389, G:G.411, G:G.412, M:T.74, M:N.132 Water bridges: G:T.182, G:T.182, G:K.186, G:K.186, G:K.186, G:G.388, G:I.390, G:I.390, G:I.390, M:E.69 Salt bridges: G:K.184, G:K.184, G:K.186, G:R.303, G:H.335, G:K.342, G:K.342 CAP.10: 22 residues within 4Å: Chain C: E.69, T.74, W.75, N.132 Chain I: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Ligands: MG.9 27 PLIP interactions: 25 interactions with chain I, 2 interactions with chain C Hydrogen bonds: I:K.184, I:D.212, I:S.387, I:G.388, I:G.389, I:G.411, I:G.412, C:T.74, C:N.132 Water bridges: I:T.182, I:T.182, I:K.186, I:K.186, I:H.335, I:G.337, I:K.342, I:K.342, I:I.390, I:I.390, I:I.390 Salt bridges: I:K.184, I:K.184, I:K.186, I:R.303, I:H.335, I:K.342, I:K.342 CAP.12: 22 residues within 4Å: Chain A: E.69, T.74, W.75, N.132 Chain K: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Ligands: MG.11 28 PLIP interactions: 26 interactions with chain K, 2 interactions with chain A Hydrogen bonds: K:T.182, K:K.184, K:D.212, K:G.388, K:G.389, K:G.411, K:G.412, A:T.74, A:N.132 Water bridges: K:T.182, K:T.182, K:K.186, K:K.186, K:G.337, K:K.342, K:K.342, K:S.387, K:G.388, K:I.390, K:I.390, K:I.390 Salt bridges: K:K.184, K:K.184, K:K.186, K:R.303, K:H.335, K:K.342, K:K.342 CAP.14: 22 residues within 4Å: Chain G: E.69, T.74, W.75, N.132 Chain M: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Ligands: MG.13 26 PLIP interactions: 22 interactions with chain M, 4 interactions with chain G Hydrogen bonds: M:T.182, M:K.184, M:D.212, M:G.388, M:G.389, M:G.411, M:G.412, G:T.74, G:N.132 Water bridges: M:T.182, M:T.182, M:K.342, M:K.342, M:S.387, M:I.390, M:I.390, M:I.390, G:E.69, G:E.69 Salt bridges: M:K.184, M:K.184, M:K.186, M:R.303, M:H.335, M:K.342, M:K.342 CAP.16: 22 residues within 4Å: Chain E: E.69, T.74, W.75, N.132 Chain O: T.182, K.184, K.186, K.210, D.212, E.213, H.302, R.303, H.335, K.342, L.343, S.387, G.388, G.389, Q.409, G.411, G.412 Ligands: MG.15 27 PLIP interactions: 24 interactions with chain O, 3 interactions with chain E Hydrogen bonds: O:T.182, O:K.184, O:D.212, O:S.387, O:G.388, O:G.389, O:G.411, O:G.412, E:T.74, E:N.132 Water bridges: O:T.182, O:T.182, O:K.186, O:K.186, O:K.186, O:G.388, O:I.390, O:I.390, O:I.390, E:E.69 Salt bridges: O:K.184, O:K.184, O:K.186, O:R.303, O:H.335, O:K.342, O:K.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugawara, H. et al., Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita. J.Biol.Chem. (1999)

Release Date

1999-09-27

Peptides

PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE): ACEGIKMO
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE): BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
A

K
C

M
E

O
G

B
S

D
U

F
W

H
Y

J
S

L
U

N
W

P
Y

PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)

PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)

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