SMTL ID : 1svd.2 (3 other biounits)

The structure of Halothiobacillus neapolitanus RuBisCo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-8-8-mer

Ligands

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.288, H.320, S.372 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain C: R.288, H.320, S.372 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain C: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain E: R.288, H.320, S.372 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain E: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain G: R.288, H.320, S.372 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain G: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain I: R.288, H.320, S.372 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain I: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain K: R.288, H.320, S.372 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain K: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain M: R.288, H.320, S.372 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain M: G.373, G.374, G.396, G.397 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain O: R.288, H.320, S.372 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain O: G.373, G.374, G.396, G.397 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: N.156 Chain B: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.51, B:K.89, A:N.156 Water bridges: B:S.51, B:W.56, B:K.89, A:N.156, A:N.156 GOL.6: 6 residues within 4Å: Chain C: N.156 Chain D: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.156, D:S.51, D:K.89 Water bridges: C:N.156, C:N.156, D:S.51, D:W.56, D:K.89 GOL.9: 6 residues within 4Å: Chain E: N.156 Chain F: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:N.156, F:S.51, F:K.89 Water bridges: E:N.156, E:N.156, F:S.51, F:W.56, F:K.89 GOL.12: 6 residues within 4Å: Chain G: N.156 Chain H: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:S.51, H:K.89, G:N.156 Water bridges: H:S.51, H:W.56, H:K.89, G:N.156, G:N.156 GOL.15: 6 residues within 4Å: Chain I: N.156 Chain J: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:S.51, J:K.89, I:N.156 Water bridges: J:S.51, J:W.56, J:K.89, I:N.156, I:N.156 GOL.18: 6 residues within 4Å: Chain K: N.156 Chain L: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain L, 3 interactions with chain K Hydrogen bonds: L:S.51, L:K.89, K:N.156 Water bridges: L:S.51, L:W.56, L:K.89, K:N.156, K:N.156 GOL.21: 6 residues within 4Å: Chain M: N.156 Chain N: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain N, 3 interactions with chain M Hydrogen bonds: N:S.51, N:K.89, M:N.156 Water bridges: N:S.51, N:W.56, N:K.89, M:N.156, M:N.156 GOL.24: 6 residues within 4Å: Chain O: N.156 Chain P: Y.13, E.14, S.51, W.56, K.89 8 PLIP interactions: 5 interactions with chain P, 3 interactions with chain O Hydrogen bonds: P:S.51, P:K.89, O:N.156 Water bridges: P:S.51, P:W.56, P:K.89, O:N.156, O:N.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerfeld, C.A. et al., The structure of Halothiobacillus neapolitanus RuBisCo. To be Published

Release Date

2005-04-12

Peptides

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit: ACEGIKMO
Ribulose bisphosphate carboxylase small chain: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

M
A

O
A

B
M

D
M

F
M

H
M

J
M

L
M

N
M

P
M

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

Ribulose bisphosphate carboxylase small chain

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