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Crystal structure of bacteriorhodopsin crystallized from bicelles

Analyse Crystal structure of bacteriorhodopsin crystallized from bicelles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KME
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: P02945
Ligands: RET, SQU, BGC
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bacteriorhodopsin	protein	227	78% helix, 5% strand	P02945

Ligands and binding sites

RET · Retinal · ligand · 2 copies · chains A, B
SQU · 2,10,23-trimethyl-tetracosane · ligand · 2 copies · chains A, B
BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.81	0.98	20	RET
2	126	0.80	0.98	23	RET
3	618	0.71	0.78	60	SQU, BGC

Interfaces

1 interface between chains.

A–B · 745 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (retinal Schiff base).

Compared structures

1KME · Crystal structure of bacteriorhodopsin crystallized from bicelles · the same entry in another collection · chain A against A, TM-score 1.00
P02945 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin (P02945) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02945
Elsewhere: RCSB PDB 1KME · PDBe 1KME · UniProt P02945

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