SMTL ID : 6z1d.1

Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120), Gadolinium complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-hexamer

Ligands

12 x GD: GADOLINIUM ATOM(Non-covalent)

GD.1: 1 residues within 4Å: Chain A: E.203 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.203, A:E.203 GD.2: 5 residues within 4Å: Chain A: R.37, E.178, K.184, P.210, K.211 No protein-ligand interaction detected (PLIP) GD.3: 1 residues within 4Å: Chain A: R.82 No protein-ligand interaction detected (PLIP) GD.6: 4 residues within 4Å: Chain A: R.168 Chain B: K.38, G.39 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) GD.7: 1 residues within 4Å: Chain C: E.203 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.203, C:E.203 GD.8: 5 residues within 4Å: Chain C: R.37, E.178, K.184, P.210, K.211 No protein-ligand interaction detected (PLIP) GD.9: 1 residues within 4Å: Chain C: R.82 No protein-ligand interaction detected (PLIP) GD.12: 4 residues within 4Å: Chain C: R.168 Chain D: K.38, G.39 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) GD.13: 1 residues within 4Å: Chain E: E.203 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.203, E:E.203 GD.14: 5 residues within 4Å: Chain E: R.37, E.178, K.184, P.210, K.211 No protein-ligand interaction detected (PLIP) GD.15: 1 residues within 4Å: Chain E: R.82 No protein-ligand interaction detected (PLIP) GD.18: 4 residues within 4Å: Chain E: R.168 Chain F: K.38, G.39 Ligands: ADP.17 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: F.209, P.210, K.211, Q.212 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: F.209, P.210, K.211, Q.212 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain E: F.209, P.210, K.211, Q.212 Ligand excluded by PLIP

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 20 residues within 4Å: Chain A: R.168 Chain B: Y.2, Y.3, I.4, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, L.48, I.187, I.191, I.214, D.215, S.218 Ligands: GD.6 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.3, B:G.39, B:E.40, B:G.41, B:K.42, B:T.43, B:F.44, B:S.218, A:R.168 Water bridges: B:Y.3 Salt bridges: B:K.42, A:R.168, A:R.168 pi-Stacking: B:F.44, B:F.44 ADP.11: 20 residues within 4Å: Chain C: R.168 Chain D: Y.2, Y.3, I.4, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, L.48, I.187, I.191, I.214, D.215, S.218 Ligands: GD.12 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.3, D:G.39, D:E.40, D:G.41, D:K.42, D:T.43, D:F.44, D:S.218, C:R.168 Water bridges: D:Y.3 Salt bridges: D:K.42, C:R.168, C:R.168 pi-Stacking: D:F.44, D:F.44 ADP.17: 20 residues within 4Å: Chain E: R.168 Chain F: Y.2, Y.3, I.4, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, L.48, I.187, I.191, I.214, D.215, S.218 Ligands: GD.18 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Y.3, F:G.39, F:E.40, F:G.41, F:K.42, F:T.43, F:F.44, F:S.218, E:R.168 Water bridges: F:Y.3 Salt bridges: F:K.42, E:R.168, E:R.168 pi-Stacking: F:F.44, F:F.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flecken, M. et al., Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes. Cell (2020)

Release Date

2020-09-23

Peptides

Ribulose bisphosphate carboxylase/oxygenase activase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Ribulose bisphosphate carboxylase/oxygenase activase

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