Research workbench

EPYC1(106-135) peptide-bound rubisco

Analyse EPYC1(106-135) peptide-bound rubisco in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JSX
Type: protein
Length: 4,832 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
EC: 4.1.1.39
UniProt: A0A218N8A3, P08475, A0A2K3DA85
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 3 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	444	43% helix, 18% strand	A0A218N8A3
B, D, F, H, J, L, N, P	Ribulose bisphosphate carboxylase small chain 2, chloroplastic (EC 4.1.1.39)	protein	138	26% helix, 22% strand	P08475
q, r, s, t, u, v, w, x	EPYC1	protein	22	41% helix, 0% strand	A0A2K3DA85

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	1034	0.86	0.87	122	empty
2	1034	0.86	0.87	128	empty
3	1066	0.85	0.86	123	empty
4	1048	0.85	0.86	125	empty
5	1057	0.85	0.86	126	empty

Interfaces

64 interfaces between chains.

E–G · 3162 Å² buried · 65 hydrogen bonds · protein-protein
M–O · 3161 Å² buried · 65 hydrogen bonds · protein-protein
I–K · 3155 Å² buried · 65 hydrogen bonds · protein-protein
A–C · 3148 Å² buried · 67 hydrogen bonds · protein-protein
A–P · 1986 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7JSX · EPYC1(106-135) peptide-bound Rubisco · the same entry in another collection · chain H against H, 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 A0A218N8A3
Every structure of UniProt P08475
Every structure of UniProt A0A2K3DA85
Elsewhere: RCSB PDB 7JSX · PDBe 7JSX · UniProt A0A218N8A3 · UniProt P08475 · UniProt A0A2K3DA85

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.