Research workbench

EPYC1(49-72)-bound rubisco

Analyse EPYC1(49-72)-bound rubisco in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JFO
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: P00877, P08475, Q94ET8
Pockets: 20 · best druggability 0.85

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	P00877
B, D, F, H, J, L, N, P	Ribulose bisphosphate carboxylase small chain 2, chloroplastic (EC 4.1.1.39)	protein	138	25% helix, 22% strand	P08475
q, r, s, t, u, v, w, x	LCI5	protein	22	41% helix, 0% strand	Q94ET8

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	1038	0.85	0.86	122	empty
2	1066	0.85	0.86	121	empty
3	1033	0.85	0.86	122	empty
4	1079	0.85	0.86	124	empty
5	1051	0.85	0.86	125	empty

Interfaces

64 interfaces between chains.

M–O · 3169 Å² buried · 65 hydrogen bonds · protein-protein
E–G · 3169 Å² buried · 65 hydrogen bonds · protein-protein
I–K · 3164 Å² buried · 65 hydrogen bonds · protein-protein
A–C · 3148 Å² buried · 67 hydrogen bonds · protein-protein
K–N · 1972 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (methylation).

Compared structures

7JFO · EPYC1(49-72)-bound Rubisco · the same entry in another collection · chain K against K, 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 P00877
Every structure of UniProt P08475
Every structure of UniProt Q94ET8
Elsewhere: RCSB PDB 7JFO · PDBe 7JFO · UniProt P00877 · UniProt P08475 · UniProt Q94ET8

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