GL1X · GenesisL1 explorer

MolNFT v1 · #10634 · protein

Crystal structure of the K intermediate of bacteriorhodopsin

1IXF: “Crystal structure of the K intermediate of bacteriorhodopsin”. X-ray diffraction, 6 ligands (L3P, RET, L2P), 1 pocket (best druggability 0.80). MolNFT v1 #10634 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1IXF
Type
protein
Length
227 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Bacteriorhodopsin
UniProt
P02945
Ligands
L3P, RET, L2P, GLC, MAN, GAL
Pockets
1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 75% helix, 4% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABacteriorhodopsinprotein22775% helix, 4% strandP02945

Ligands and binding sites

  • L3P · 2,3-di-O-phytanly-3-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-phosphate · ligand · 4 copies · chains A
  • RET · Retinal · ligand · chains A
  • L2P · 2,3-di-phytanyl-glycerol · ligand · chains A
  • GLC · alpha-D-glucopyranose · sugar · chains A
  • MAN · alpha-D-mannopyranose · sugar · chains A
  • GAL · beta-D-galactopyranose · sugar

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11350.800.9726RET

Modifications

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

Compared structures

  • 1IXF · Crystal Structure of the K intermediate of 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

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