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Cryoem structure of rubisco activase with its substrate rubisco from nostoc sp. (strain PCC7120)

Analyse Cryoem structure of rubisco activase with its substrate rubisco from nostoc sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z1F
Type: protein
Length: 6,255 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase; Ribulose bisphosphate carboxylase…
EC: 4.1.1.39
UniProt: P58555, P00879, P06514
Ligands: CAP, AGS, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 8 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 5	Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase	protein	280	50% helix, 9% strand	P58555
2, 4	Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase	protein	281	45% helix, 10% strand	P58555
3	Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase	protein	284	46% helix, 11% strand	P58555
6	Ribulose bisphosphate CARBOXYLASE/OXYGENASE activase	protein	276	49% helix, 10% strand	P58555
A	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	466	39% helix, 18% strand	P00879
B	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	459	41% helix, 18% strand	P00879
C, D, E, F, G, H	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	464	41% helix, 17% strand	P00879
I, J, K, L, M, N, O, P	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39)	protein	108	26% helix, 24% strand	P06514

Ligands and binding sites

CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G, H
AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains 2, 3, 4, 5, 6, 1
ADP · Adenosine-5'-diphosphate · ligand · chains 1
MG · Magnesium ion · metal · 12 copies · chains 2, 3, 4, 5, 6, A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.87	0.88	149	empty
2	965	0.87	0.88	150	empty
3	247	0.84	0.96	50	MG, CAP
4	233	0.84	0.97	48	CAP
5	238	0.83	0.96	49	MG, CAP

Interfaces

70 interfaces between chains.

G–H · 4950 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 4940 Å² buried · 53 hydrogen bonds · protein-protein
E–F · 4926 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 4158 Å² buried · 43 hydrogen bonds · protein-protein
4–5 · 2794 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 4 disulfide (carboxylation, disulfide).

Compared structures

P00879 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain C against A, TM-score 0.99
P06514 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain I against A, TM-score 0.98
P58555 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate CARBOXYLASE/OXYGENASE… · a predicted model of the same protein · chain 2 against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P58555
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Every structure of UniProt P06514
Elsewhere: RCSB PDB 6Z1F · PDBe 6Z1F · UniProt P58555 · UniProt P00879 · UniProt P06514

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