Research workbench

Ribosome-bound secyeg translocon in a nanodisc

Analyse Ribosome-bound secyeg translocon in a nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R7L
Type: protein
Length: 521 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Secg; SECE,PROTEIN translocase subunit SECE,PROTEIN translocase subunit SECE,PROTEIN…
UniProt: A0A377BMD6, P0AGA2
Pockets: 3 · best druggability 0.78

Structure

electron microscopy · 3 distinct chains · 70% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Secg	protein	22	91% helix, 0% strand	—
E	SECE,PROTEIN translocase subunit SECE,PROTEIN translocase subunit SECE,PROTEIN translocase subunit sece	protein	98	83% helix, 0% strand	A0A377BMD6
Y	Protein translocase subunit secy	protein	401	66% helix, 4% strand	P0AGA2

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.78	0.80	124	empty
2	243	0.59	0.79	46	empty
3	101	0.38	0.76	32	empty

Interfaces

2 interfaces between chains.

E–Y · 466 Å² buried · 0 hydrogen bonds · protein-protein
G–Y · 46 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6R7L · Ribosome-bound SecYEG translocon in a nanodisc · the same entry in another collection · chain G against G, TM-score 1.00
P0AGA2 · AlphaFold monomer V2.0 prediction for protein translocase subunit secy (P0AGA2) · a predicted model of the same protein · chain Y against A, TM-score 0.90

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 A0A377BMD6
Every structure of UniProt P0AGA2
Elsewhere: RCSB PDB 6R7L · PDBe 6R7L · UniProt A0A377BMD6 · UniProt P0AGA2

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