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Structure of marine actinobacteria clade rhodopsin (macr) in violet form

Analyse Structure of marine actinobacteria clade rhodopsin (macr) in violet form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AVP
Type: protein
Length: 217 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: S5DM51
Ligands: LFA
Pockets: 1 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriorhodopsin	protein	217	86% helix, 0% strand	S5DM51

Ligands and binding sites

LFA · Eicosane · ligand · 18 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.44	0.81	19	empty

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

7AVP · Structure of marine actinobacteria clade rhodopsin (MacR) in violet form · the same entry in another collection · chain A against A, TM-score 1.00

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 S5DM51
Elsewhere: RCSB PDB 7AVP · PDBe 7AVP · UniProt S5DM51

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