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Cryo-EM structure of RuBisCO-Raf1 from Anabaena sp. PCC 7120

Analyse Cryo-EM structure of RuBisCO-Raf1 from Anabaena sp. PCC 7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LRR
Type: protein
Length: 5,494 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.37
Source: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
Molecule: All5250 protein; Ribulose bisphosphate carboxylase small chain; Ribulose bisphosphate…
EC: 4.1.1.39
UniProt: Q8YLP6, P06514, P00879
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · resolution 3.37 · 7 distinct chains · 28% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, M, K, I	All5250 protein	protein	141	5% helix, 34% strand	Q8YLP6
P, N, L, J	All5250 protein	protein	157	8% helix, 32% strand	Q8YLP6
T, U, X, Q	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39)	protein	106	23% helix, 23% strand	P06514
W, V, Y, R	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39)	protein	105	23% helix, 19% strand	P06514
G, E, A	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	430	33% helix, 17% strand	P00879
H, F, D, B	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	434	34% helix, 16% strand	P00879
C	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	432	33% helix, 17% strand	P00879

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	1012	0.82	0.83	89	empty
2	1123	0.81	0.83	89	empty
3	1158	0.81	0.82	92	empty
4	1192	0.80	0.82	103	empty
5	697	0.80	0.85	58	empty

Interfaces

68 interfaces between chains.

C–D · 3170 Å² buried · 45 hydrogen bonds · protein-protein
G–H · 3077 Å² buried · 44 hydrogen bonds · protein-protein
E–F · 3054 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 3048 Å² buried · 43 hydrogen bonds · protein-protein
I–J · 2769 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6LRR · Cryo-EM structure of rubisco-RAF1 from anabaena sp. pcc 7120 · the same entry in another collection · chain J against J, TM-score 1.00

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 Q8YLP6
Every structure of UniProt P06514
Every structure of UniProt P00879
Elsewhere: RCSB PDB 6LRR · PDBe 6LRR · UniProt Q8YLP6 · UniProt P06514 · UniProt P00879

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