SMTL ID : 5c2g.1

GWS1B RubisCO: Form II RubisCO derived from uncultivated Gallionellacea species (CABP-bound).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

CAP.1: 23 residues within 4Å: Chain A: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Chain C: E.68, T.73, N.131 Ligands: MG.2 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:K.186, A:H.307, A:H.311, A:S.388, A:S.388, A:S.388, A:G.389, A:G.390, A:G.413, A:G.414, C:T.73, C:T.73, C:N.131 Water bridges: A:R.308, A:R.308, A:G.415 Salt bridges: A:K.186, A:K.186, A:K.188, A:R.308, A:H.341, A:K.349, A:K.349 CAP.3: 24 residues within 4Å: Chain B: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Chain F: E.68, T.73, N.74, N.131 Ligands: MG.4 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:K.186, B:H.307, B:H.311, B:S.388, B:S.388, B:S.388, B:G.390, B:G.413, B:G.414, F:T.73, F:T.73, F:N.131 Water bridges: B:H.341, B:G.343, B:G.389, B:G.415 Salt bridges: B:K.186, B:K.186, B:K.188, B:R.308, B:H.341, B:K.349, B:K.349 CAP.5: 23 residues within 4Å: Chain A: E.68, T.73, N.131 Chain C: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Ligands: MG.6 23 PLIP interactions: 20 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.186, C:H.307, C:H.311, C:S.388, C:S.388, C:S.388, C:G.390, C:G.413, C:G.414, A:T.73, A:T.73, A:N.131 Water bridges: C:R.308, C:G.343, C:S.388, C:G.415 Salt bridges: C:K.186, C:K.186, C:K.188, C:R.308, C:H.341, C:K.349, C:K.349 CAP.7: 23 residues within 4Å: Chain D: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Chain E: E.68, T.73, N.131 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:K.186, D:H.307, D:H.311, D:S.388, D:S.388, D:S.388, D:G.390, D:G.413, D:G.414, E:T.73, E:T.73, E:N.131 Water bridges: D:V.342, D:G.343 Salt bridges: D:K.186, D:K.186, D:K.188, D:R.308, D:H.341, D:K.349, D:K.349 CAP.9: 24 residues within 4Å: Chain D: E.68, T.73, N.74, N.131 Chain E: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Ligands: MG.10 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:K.186, E:H.307, E:H.311, E:S.388, E:S.388, E:G.390, E:G.413, E:G.414, D:T.73, D:T.73, D:N.131 Water bridges: E:G.389, E:M.391 Salt bridges: E:K.186, E:K.186, E:K.188, E:R.308, E:H.341, E:K.349, E:K.349 CAP.11: 23 residues within 4Å: Chain B: E.68, T.73, N.131 Chain F: I.184, K.186, K.188, K.211, D.213, E.214, H.307, R.308, H.311, H.341, G.343, K.349, M.350, S.388, G.389, G.390, A.412, G.413, G.414 Ligands: MG.12 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain F Hydrogen bonds: B:T.73, B:N.131, F:K.186, F:H.307, F:H.311, F:S.388, F:S.388, F:S.388, F:G.390, F:G.413, F:G.414 Water bridges: F:M.391, F:M.391, F:G.415 Salt bridges: F:K.186, F:K.186, F:K.188, F:R.308, F:H.341, F:K.349, F:K.349

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 9 residues within 4Å: Chain A: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Chain C: N.131 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.213, A:E.214 MG.4: 9 residues within 4Å: Chain B: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Chain F: N.131 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.213, B:E.214 MG.6: 9 residues within 4Å: Chain A: N.131 Chain C: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Ligands: CAP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.213, C:D.213, C:E.214 MG.8: 9 residues within 4Å: Chain D: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Chain E: N.131 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.213, D:E.214 MG.10: 9 residues within 4Å: Chain D: N.131 Chain E: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Ligands: CAP.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.213, E:D.213, E:E.214 MG.12: 9 residues within 4Å: Chain B: N.131 Chain F: I.184, K.186, K.188, K.211, D.213, E.214, H.307 Ligands: CAP.11 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.213, F:D.213, F:E.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varaljay, V.A. et al., Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria. Environ.Microbiol. (2016)

Release Date

2015-12-16

Peptides

Form II RubisCO: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Form II RubisCO

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