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Crystal structure of bacteriorhodopsin at 1.25 a resolution

Analyse Crystal structure of bacteriorhodopsin at 1.25 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZIM
Type: protein
Length: 228 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: P02945
Ligands: L2P, RET
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriorhodopsin	protein	228	74% helix, 5% strand	P02945

Ligands and binding sites

L2P · 2,3-di-phytanyl-glycerol · ligand · 4 copies · chains A
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	112	0.81	0.99	23	RET
2	54	0.29	0.75	16	empty

Modifications

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

Compared structures

5ZIM · Crystal structure of bacteriorhodopsin at 1.25 A resolution · 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 5ZIM · PDBe 5ZIM · UniProt P02945

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