MolNFT v1 · #129906 · protein

Unusual posttranslational modifications revealed in crystal structures of diatom rubisco.

5OYA · Rubisco large subunit: “Unusual posttranslational modifications revealed in crystal structures of diatom rubisco.”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #129906 on GenesisL1: 3D…

PDB: 5OYA
Type: protein
Length: 4,860 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rubisco large subunit; Rubisco small subunit
Ligands: CAP, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, H	Rubisco large subunit	protein	468	42% helix, 16% strand	—
B, E, F, G	Rubisco large subunit	protein	469	42% helix, 16% strand	—
I, J, K, L, M, N, O, P	Rubisco small subunit	protein	139	23% helix, 29% strand	—

Ligands and binding sites

CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, K, N
EDO · 1,2-ethanediol · additive · 24 copies · chains A, G, I, L, C, J, E, K, B, H, M, P, D, N, F, O

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	284	0.81	0.93	51	empty
2	285	0.81	0.92	50	empty
3	794	0.81	0.84	115	empty
4	635	0.80	0.85	84	empty
5	873	0.80	0.82	105	EDO, MG

Interfaces

41 interfaces between chains.

A–I · 1602 Å² buried · 20 hydrogen bonds · protein-protein
B–M · 1601 Å² buried · 17 hydrogen bonds · protein-protein
D–N · 1599 Å² buried · 17 hydrogen bonds · protein-protein
G–L · 1598 Å² buried · 20 hydrogen bonds · protein-protein
E–K · 1598 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 63 modified (nonstandard, hydroxylation, carboxylation, methylation, oxidation).

Compared structures

5OYA · Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco. · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 5OYA · PDBe 5OYA

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