MolNFT v1 · #1039 · protein

X-ray structure of bacteriorhodopsin from microcrystals grown in lipidic cubic phases

1AP9: “X-ray structure of bacteriorhodopsin from microcrystals grown in lipidic cubic phases”. X-ray diffraction, 1 ligand (RET), 2 pockets (best druggability 0.80). MolNFT v1 #1039 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1AP9
Type: protein
Length: 219 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 · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriorhodopsin	protein	219	66% helix, 0% 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	129	0.80	0.97	26	RET
2	100	0.39	0.76	15	empty

Modifications

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

Compared structures

1AP9 · X-ray structure of bacteriorhodopsin from microcrystals grown in lipidic cubic phases · 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 0.95

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 1AP9 · PDBe 1AP9 · UniProt P02945

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