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Structure of bacteriorhodopsin from crystals grown at 4 deg C using GLYNCOC15+4 as an lcp host lipid

Analyse Structure of bacteriorhodopsin from crystals grown at 4 deg C using GLYNCOC15+4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VN9
Type: protein
Length: 452 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: P02945
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bacteriorhodopsin	protein	226	77% helix, 4% strand	P02945

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.61	0.87	20	empty
2	106	0.56	0.84	15	empty
3	115	0.55	0.82	16	empty
4	191	0.47	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 726 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5VN9 · Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP… · 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 B 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 5VN9 · PDBe 5VN9 · UniProt P02945

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