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High resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle

Analyse High resolution X-ray structure of an early intermediate in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QKO
Type: protein
Length: 228 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: P02945
Ligands: RET
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriorhodopsin	protein	228	77% helix, 5% strand	P02945

Ligands and binding sites

RET · Retinal · ligand · chains A

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	121	0.80	0.97	23	RET
2	55	0.29	0.75	14	empty

Modifications

Observed in the structure: 1 cofactor (retinal Schiff base).

Compared structures

1QKO · High resolution X-ray structure of an early intermediate in the bacteriorhodopsin… · 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

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 P02945
Elsewhere: RCSB PDB 1QKO · PDBe 1QKO · UniProt P02945

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