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Structure of membrane protein

Analyse Structure of membrane protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JSI
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: S5DM51
Ligands: LFA, IOD
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bacteriorhodopsin	protein	215	86% helix, 0% strand	S5DM51

Ligands and binding sites

LFA · Eicosane · ligand · 22 copies · chains A, B
IOD · Iodide ion · ion · 22 copies · chains A, B
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	946	0.73	0.77	64	LFA, IOD
2	56	0.30	0.75	15	IOD

Interfaces

1 interface between chains.

A–B · 180 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5JSI · Structure of membrane protein · 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
Every structure of UniProt S5DM51
Elsewhere: RCSB PDB 5JSI · PDBe 5JSI · UniProt S5DM51

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